Thu, 21 Aug 2008 15:37:08 BST CiteULike: balicea's comparative-neuro http://www.citeulike.org/user/balicea/tag/comparative-neuro CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/balicea/article/540888 <i>Nature, Vol. 440, No. 7081. (March 2006), pp. 161-161.</i> Comparative genomics: Difference of expression Rasmus Nielsen doi:10.1038/440161a Nature, Vol. 440, No. 7081. (March 2006), pp. 161-161. 2006-03-08T21:23:33-00:00 2006 Nature 440 7081 161 161 comparative-neuro evolution evolvability functional-genome gene-expression regulatory-cascades speciation http://www.citeulike.org/user/balicea/article/2954033 <i>Journal of integrative neuroscience, Vol. 6, No. 3. (September 2007), pp. 433-446.</i><br /><br />The grid cells of the rodent medial entorhinal cortex (MEC) show activity patterns correlated with the animal's position. Unlike hippocampal place cells that are activated at only one specific location in the environment, MEC grid cells increase firing frequency at multiple regions in space, or subfields, that are arranged in regular triangular grids. It has been recently shown that a conjunction of MEC grid cells can lead to unique spatial representations. However, it remains unclear what the key properties of the grids are that allow for an accurate reconstruction of the position of the animal and what the comparison with hippocampal place cells is. Here we use a theoretical approach based on data from electrophysiological recordings of the MEC to simulate the neural activity of grid cells. Our simulations account for the accurate reproduction of grid cell mean firing rates, based on only three grid parameters, that is grid phase, spacing and orientation. The analysis of the key properties of the grids first reveals that for an accurate position reconstruction, it is necessary to combine cells with different grid spacings (which are found at different dorsoventral locations of the MEC) or orientations. Second, the relationship between grid spacing and subfield size observed in physiological data is optimal to predict the animal's position. Third, the regular triangular tessellating patterns of grid cells lead to the best position reconstruction results when compared with all other regular tessellations of two-dimensional space. Finally, the comparison of grid cells with place cells shows that populations of MEC grid cells can better predict the animal's position than equally-sized populations of hippocampal place cells with similar but unique spatial fields. Taken together, our results suggest that the MEC provides highly compact representations of the animal's position, which may be subsequently integrated by the place cells of the hippocampus. Prediction of the position of an animal based on populations of grid and place cells: a comparative simulation study. A Guanella PF Verschure Journal of integrative neuroscience, Vol. 6, No. 3. (September 2007), pp. 433-446. 2008-07-02T22:02:53-00:00 2007 Journal of integrative neuroscience 0219-6352 6 3 433 446 animal-model cell-models cog-neuro comparative-neuro modeling-and-simulation neuro-morphic robotics http://www.citeulike.org/user/balicea/article/2910641 <i>Mechanisms, Symbols, and Models Underlying Cognition (2005), pp. 346-355.</i><br /><br />We have developped a mobile robot control system based on hippocampus and prefrontal models. We propose an alternative to models that rely on cognitive maps linking place cells. Our experiments show that using transition cells is more efficient than using place cells. The transition cell links two locations with the integrated direction used. Furthermore, it is possible to fuse the different directions proposed by nearby transitions and obstacles into an effective direction by using a Neural Field. The direction to follow is the stable fixed point of the Neural Field dynamics, and its derivative gives the angular rotation speed. Simulations and robotics experiments are carried out. Transition Cells and Neural Fields for Navigation and Planning Nicolas Cuperlier Mathias Quoy Philippe Laroque Philippe Gaussier doi:10.1007/11499220_36 Mechanisms, Symbols, and Models Underlying Cognition (2005), pp. 346-355. 2008-06-20T14:54:54-00:00 2005 Mechanisms, Symbols, and Models Underlying Cognition 346 355 biological-inspired-modeling cell-models cog-neuro comparative-neuro evolution-of-intelligence neuro-coding neuro-computation neuro-morphic neuro-spike robotics spatial-cognition http://www.citeulike.org/user/balicea/article/2879868 <i>Nature neuroscience (8 June 2008)</i><br /><br />Understanding the origins and evolution of synapses may provide insight into species diversity and the organization of the brain. Using comparative proteomics and genomics, we examined the evolution of the postsynaptic density (PSD) and membrane-associated guanylate kinase (MAGUK)-associated signaling complexes (MASCs) that underlie learning and memory. PSD and MASC orthologs found in yeast carry out basic cellular functions to regulate protein synthesis and structural plasticity. We observed marked changes in signaling complexity at the yeast-metazoan and invertebrate-vertebrate boundaries, with an expansion of key synaptic components, notably receptors, adhesion/cytoskeletal proteins and scaffold proteins. A proteomic comparison of Drosophila and mouse MASCs revealed species-specific adaptation with greater signaling complexity in mouse. Although synaptic components were conserved amongst diverse vertebrate species, mapping mRNA and protein expression in the mouse brain showed that vertebrate-specific components preferentially contributed to differences between brain regions. We propose that the evolution of synapse complexity around a core proto-synapse has contributed to invertebrate-vertebrate differences and to brain specialization. Evolutionary expansion and anatomical specialization of synapse proteome complexity. Richard D Emes Andrew J Pocklington Christopher N G Anderson Alex Bayes Mark O Collins Catherine A Vickers Mike D R Croning Bilal R Malik Jyoti S Choudhary J Douglas Armstrong Seth G N Grant doi:10.1038/nn.2135 Nature neuroscience (8 June 2008) 2008-06-10T15:04:10-00:00 2008 Nature neuroscience 1097-6256 animal-model brain-anatomy comparative-neuro evolution evolutionary-proteomics evolution-of-intelligence evolvability molecular-signaling neuro-computation phylogeny synaptic-complexity http://www.citeulike.org/user/balicea/article/2895205 <i>Cerebral cortex (New York, N.Y. : 1991) (11 June 2008)</i><br /><br />We recently identified the thalamic dopaminergic system in the human and macaque monkey brains, and, based on earlier reports on the paucity of dopamine in the rat thalamus, hypothesized that this dopaminergic system was particularly developed in primates. Here we test this hypothesis using immunohistochemistry against the dopamine transporter (DAT) in adult macaque and rat brains. The extent and density of DAT-immunoreactive (-ir) axons were remarkably greater in the macaque dorsal thalamus, where the mediodorsal association nucleus and the ventral motor nuclei held the densest immunolabeling. In contrast, sparse DAT immunolabeling was present in the rat dorsal thalamus; it was mainly located in the mediodorsal, paraventricular, ventral medial, and ventral lateral nuclei. The reticular nucleus, zona incerta, and lateral habenular nucleus held numerous DAT-ir axons in both species. Ultrastructural analysis in the macaque mediodorsal nucleus revealed that thalamic interneurons are a main postsynaptic target of DAT-ir axons; this suggests that the marked expansion of the dopamine innervation in the primate in comparison to the rodent thalamus may be related to the presence of a sizable interneuron population in primates. We remark that it is important to be aware of brain species differences when using animal models of human brain disease. Dopamine Innervation in the Thalamus: Monkey versus Rat. Miguel Ángel García-Cabezas Patricia Martínez-Sánchez Miguel Ángel Sánchez-González Miguel Garzón Carmen Cavada Cerebral cortex (New York, N.Y. : 1991) (11 June 2008) 2008-06-15T00:47:52-00:00 2008 Cerebral cortex (New York, N.Y. : 1991) 1460-2199 animal-model brain-anatomy comparative-neuro neuro-chem phylogeny http://www.citeulike.org/user/balicea/article/828634 <i>J. Neural Eng., Vol. 3, No. 4. (December 2006), 257.</i> A silicon retina that reproduces signals in the optic nerve Kareem Zaghloul Kwabena Boahen doi:10.1088/1741-2560/3/4/002 J. Neural Eng., Vol. 3, No. 4. (December 2006), 257. 2006-09-05T15:01:08-00:00 2006 J. Neural Eng. 1741-2552 3 4 257 Institute of Physics Publishing brain-anatomy comparative-neuro complexity neuro-coding neuro-computation neuro-morphic neuro-spike neuro-tech robotics sensory-systems http://www.citeulike.org/user/balicea/article/1199644 <i>Trends in Genetics, Vol. 23, No. 4. (April 2007), pp. 200-207.</i><br /><br />The use of cross-species hybridization (CSH) to DNA microarrays, in which the target RNA and microarray probe are from different species, has increased in the past few years. CSH is used in comparative, evolutionary and ecological studies of closely related species, and for gene-expression profiling of many species that lack a representative microarray platform. However, unlike species-specific hybridization, CSH is still considered a non-standard use of microarrays. Here, we present the recent developments in the field of CSH for cDNA and oligomer microarray platforms. We discuss issues that influence the quality of CSH results, including platform choice, experiment design and data analysis, and suggest strategies that can lead to improvement of CSH studies to investigate species diversity. Cross-species microarray hybridizations: a developing tool for studying species diversity Carmiya Bar-Or Henryk Czosnek Hinanit Koltai doi:10.1016/j.tig.2007.02.003 Trends in Genetics, Vol. 23, No. 4. (April 2007), pp. 200-207. 2007-03-31T12:40:31-00:00 2007 Trends in Genetics 23 4 200 207 animal-model comparative-neuro evo-tech reviews systems-biology http://www.citeulike.org/user/balicea/article/1044702 <i>Human Mutation, Vol. 28, No. 2. (2007), pp. 99-130.</i><br /><br />The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome. Hum Mutat 28(2), 99-130, 2007. © 2006 Wiley-Liss, Inc. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons Hildegard Kehrer-Sawatzki David Cooper doi:10.1002/humu.20420 Human Mutation, Vol. 28, No. 2. (2007), pp. 99-130. 2007-01-16T17:58:20-00:00 2007 Human Mutation 28 2 99 130 animal-model comparative-neuro evolution evolutionary-genomics genome-sequencing genome-structure http://www.citeulike.org/user/balicea/article/2275734 <i>PLoS Biology, Vol. 3, No. 11. (2005), e357.</i><br /><br />The origin of new genes through gene duplication is fundamental to the evolution of lineage- or species-specific phenotypic traits. In this report, we estimate the number of functional retrogenes on the lineage leading to humans generated by the high rate of retroposition (retroduplication) in primates. Extensive comparative sequencing and expression studies coupled with evolutionary analyses and simulations suggest that a significant proportion of recent retrocopies represent bona fide human genes. We estimate that at least one new retrogene per million years emerged on the human lineage during the past approximately 63 million years of primate evolution. Detailed analysis of a subset of the data shows that the majority of retrogenes are specifically expressed in testis, whereas their parental genes show broad expression patterns. Consistently, most retrogenes evolved functional roles in spermatogenesis. Proteins encoded by X chromosome-derived retrogenes were strongly preserved by purifying selection following the duplication event, supporting the view that they may act as functional autosomal substitutes during X-inactivation of late spermatogenesis genes. Also, some retrogenes acquired a new or more adapted function driven by positive selection. We conclude that retroduplication significantly contributed to the formation of recent human genes and that most new retrogenes were progressively recruited during primate evolution by natural and/or sexual selection to enhance male germline function. Emergence of young human genes after a burst of retroposition in primates. AC Marques I Dupanloup N Vinckenbosch A Reymond H Kaessmann PLoS Biology, Vol. 3, No. 11. (2005), e357. 2008-01-22T18:46:22-00:00 2005 PLoS Biology 3 11 e357 comparative-neuro evolution evolutionary-genomics evolvability genome-association genome-transposon genome-variation phylogeny http://www.citeulike.org/user/balicea/article/2269803 <i>Nat Neurosci, Vol. 6, No. 4. (April 2003), pp. 341-342.</i><br /><br />Animals that rely on acoustic communication to find mates, such as grasshoppers, are astonishingly accurate in recognizing song patterns that are specific to their own species1, 2. This raises the question of whether they can also solve a far more complicated task that might provide a basis for mate preference and sexual selection: to distinguish individual songs by detecting slight variations around the common species-specific theme. Using spike-train discriminability to quantify the precision of neural responses from the auditory periphery of a model grasshopper species, we show that information sufficient to distinguish songs is readily available at the single-cell level when the spike trains are analyzed on a millisecond time scale. Single auditory neurons rapidly discriminate conspecific communication signals. CK Machens H Schütze A Franz O Kolesnikova MB Stemmler B Ronacher AV Herz doi:10.1038/nn1036 Nat Neurosci, Vol. 6, No. 4. (April 2003), pp. 341-342. 2008-01-21T19:26:30-00:00 2003 Nat Neurosci 1097-6256 6 4 341 342 brain-anatomy cog-neuro comparative-neuro neuro-coding neuro-computation neuroethology neuro-evolution neuro-timing perception http://www.citeulike.org/user/balicea/article/2220461 <i>J Neurosci, Vol. 28, No. 1. (2 January 2008), pp. 249-257.</i><br /><br />In higher mammals, environmentally driven patterns of neural activity do not play a role in the establishment of orientation specificity and maps. It has been proposed that specific long-range interactions provide the scaffold for developing orientation maps. Our model aims at explaining how such a scaffold could develop in the first place. Broad spontaneous activity waves and locally evoked spatially periodic response pattern are used. The model is discussed in relation to biological evidence, and experiments to test the model are proposed. We show that reliable orientation specificity cannot be a result of haphazard cortical wiring, as has been proposed. Establishment of a scaffold for orientation maps in primary visual cortex of higher mammals. A Grabska-Barwinska C von der Malsburg doi:10.1523/JNEUROSCI.5514-06.2008 J Neurosci, Vol. 28, No. 1. (2 January 2008), pp. 249-257. 2008-01-11T18:36:30-00:00 2008 J Neurosci 1529-2401 28 1 249 257 animal-model brain-anatomy comparative-neuro neuro-connectivity neuro-evolution neuroplasticity http://www.citeulike.org/user/balicea/article/1978158 <i>Genome Res (21 November 2007)</i><br /><br />Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional genomic factors to the variation in mutability among orthologous human-chimpanzee microsatellites are investigated with resampling and regression techniques. As a result, we uncover the intricacies of microsatellite mutagenesis as follows. First, intrinsic features (repeat number, length, and motif size), which all influence the probability and rate of slippage, are the strongest predictors of mutability. Second, mutability increases nonuniformly with length, suggesting that processes additional to slippage, such as faulty repair, contribute to mutations. Third, mutability varies among microsatellites with different motif composition likely due to dissimilarities in secondary DNA structure formed by their slippage intermediates. Fourth, mutability of mononucleotide microsatellites is impacted by their location on sex chromosomes vs. autosomes and inside vs. outside of Alu repeats, the former confirming the importance of replication and the latter suggesting a role for gene conversion. Fifth, transcription status and location in a particular isochore do not influence microsatellite mutability. Sixth, compared with intrinsic features, regional genomic factors have only minor effects. Finally, our regression models explain approximately 90% of variation in microsatellite mutability and can generate useful predictions for the studies of human diseases, forensics, and conservation genetics. The genome-wide determinants of human and chimpanzee microsatellite evolution. Yogeshwar D Kelkar Svitlana Tyekucheva Francesca Chiaromonte Kateryna D Makova doi:10.1101/gr.7113408 Genome Res (21 November 2007) 2007-11-25T06:26:11-00:00 2007 Genome Res 1088-9051 animal-model comparative-neuro evolution evolutionary-genomics genome-structure genome-variation whole-genomic http://www.citeulike.org/user/balicea/article/2188557 <i>Curr Biol, Vol. 17, No. 19. (9 October 2007), pp. 1663-1668.</i><br /><br />To make adaptive choices, individuals must sometimes exhibit patience, forgoing immediate benefits to acquire more valuable future rewards [1-3]. Although humans account for future consequences when making temporal decisions [4], many animal species wait only a few seconds for delayed benefits [5-10]. Current research thus suggests a phylogenetic gap between patient humans and impulsive, present-oriented animals [9, 11], a distinction with implications for our understanding of economic decision making [12] and the origins of human cooperation [13]. On the basis of a series of experimental results, we reject this conclusion. First, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes) exhibit a degree of patience not seen in other animals tested thus far. Second, humans are less willing to wait for food rewards than are chimpanzees. Third, humans are more willing to wait for monetary rewards than for food, and show the highest degree of patience only in response to decisions about money involving low opportunity costs. These findings suggest that core components of the capacity for future-oriented decisions evolved before the human lineage diverged from apes. Moreover, the different levels of patience that humans exhibit might be driven by fundamental differences in the mechanisms representing biological versus abstract rewards. The evolutionary origins of human patience: temporal preferences in chimpanzees, bonobos, and human adults. AG Rosati JR Stevens B Hare MD Hauser doi:10.1016/j.cub.2007.08.033 Curr Biol, Vol. 17, No. 19. (9 October 2007), pp. 1663-1668. 2008-01-02T15:54:02-00:00 2007 Curr Biol 0960-9822 17 19 1663 1668 animal-model behavior comparative-neuro cultural-evolution evolution evolution-of-intelligence neuroethology time-course http://www.citeulike.org/user/balicea/article/808896 <i>Nature Reviews Genetics, Vol. 7, No. 9., pp. 693-702.</i> Evolution of primate gene expression Philipp Khaitovich Wolfgang Enard Michael Lachmann Svante Pääbo doi:10.1038/nrg1940 Nature Reviews Genetics, Vol. 7, No. 9., pp. 693-702. 2006-08-21T07:27:23-00:00 Nature Reviews Genetics 1471-0056 7 9 693 702 Nature Publishing Group animal-model brain-anatomy comparative-neuro evolution evolutionary-genomics gene-expression genotype-to-phenotype http://www.citeulike.org/user/balicea/article/2204698 <i>Trends in Neuroscience, Vol. 17 (1994), pp. 413-420.</i> Neural architectures for adaptive behavior. D Morton H Chiel Trends in Neuroscience, Vol. 17 (1994), pp. 413-420. 2008-01-07T19:23:52-00:00 1994 Trends in Neuroscience 17 413 420 adaptive-systems biological-inspired-modeling brain-anatomy comparative-neuro neuro-computation neuroethology neuro-mechanics http://www.citeulike.org/user/balicea/article/1675496 <i>The Lancet Neurology, Vol. 6, No. 10. (October 2007), pp. 850-851.</i> Neuroproteomics comes of age James Butcher doi:10.1016/S1474-4422(07)70234-X The Lancet Neurology, Vol. 6, No. 10. (October 2007), pp. 850-851. 2007-09-19T10:09:47-00:00 2007 The Lancet Neurology 6 10 850 851 comparative-neuro evolutionary-proteomics neuro-chem neuro-evolution neuro-tech reviews http://www.citeulike.org/user/balicea/article/1881867 <i>Genome Res. (7 November 2007), gr.6249707.</i><br /><br />The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding genes were predicted using established Drosophila melanogaster genes as templates, with recovery rates ranging from 81%97% depending on species divergence and on genome assembly quality. Orthology and paralogy assignments were shown to be self-consistent among the different Drosophila species and to be consistent with regions of conserved gene order (synteny blocks). Next, we investigated the rates of diversification among these species' gene repertoires with respect to amino acid substitutions and to gene duplications. Constraints on amino acid sequences appear to have been most pronounced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages. Codons predicted to have been subject to positive selection were found to be significantly over-represented among genes with roles in immune response and RNA metabolism, with the latter category including each subunit of the Dicer-2/r2d2 heterodimer. The vast majority of gene duplications (96.5%) and synteny rearrangements were found to occur, as expected, within single Muller elements. We show that the rate of ancient gene duplications was relatively uniform. However, gene duplications in terminal lineages are strongly skewed toward very recent events, consistent with either a rapid-birth and rapid-death model or the presence of large proportions of copy number variable genes in these Drosophila populations. Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins. 10.1101/gr.6249707 Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Andreas Heger Chris Ponting doi:10.1101/gr.6249707 Genome Res. (7 November 2007), gr.6249707. 2007-11-07T23:42:51-00:00 2007 Genome Res. gr.6249707 animal-model comparative-neuro evolution evolutionary-genomics genome-variation orthologs-paralogs whole-genomic http://www.citeulike.org/user/balicea/article/2173808 <i>PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e247.</i><br /><br />Taking advantage of the complete genome sequences of several mammals, we developed a novel method to detect losses of well-established genes in the human genome through syntenic mapping of gene structures between the human, mouse, and dog genomes. Unlike most previous genomic methods for pseudogene identification, this analysis is able to differentiate losses of well-established genes from pseudogenes formed shortly after segmental duplication or generated via retrotransposition. Therefore, it enables us to find genes that were inactivated long after their birth, which were likely to have evolved nonredundant biological functions before being inactivated. The method was used to look for gene losses along the human lineage during the approximately 75 million years (My) since the common ancestor of primates and rodents (the euarchontoglire crown group). We identified 26 losses of well-established genes in the human genome that were all lost at least 50 My after their birth. Many of them were previously characterized pseudogenes in the human genome, such as GULO and UOX. Our methodology is highly effective at identifying losses of single-copy genes of ancient origin, allowing us to find a few well-known pseudogenes in the human genome missed by previous high-throughput genome-wide studies. In addition to confirming previously known gene losses, we identified 16 previously uncharacterized human pseudogenes that are definitive losses of long-established genes. Among them is ACYL3, an ancient enzyme present in archaea, bacteria, and eukaryotes, but lost approximately 6 to 8 Mya in the ancestor of humans and chimps. Although losses of well-established genes do not equate to adaptive gene losses, they are a useful proxy to use when searching for such genetic changes. This is especially true for adaptive losses that occurred more than 250,000 years ago, since any genetic evidence of the selective sweep indicative of such an event has been erased. Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage Jingchun Zhu Zachary Sanborn Mark Diekhans Craig Lowe Tom Pringle David Haussler doi:10.1371/journal.pcbi.0030247 PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e247. 2007-12-26T23:36:41-00:00 2007 PLoS Computational Biology 3 12 e247 comparative-neuro evolution evolutionary-genomics genome-variation heredity informatics phylogeny whole-genomic http://www.citeulike.org/user/balicea/article/2165125 <i>Genome Research, Vol. 14 (2004), pp. 1851-1860.</i> Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation. WC Nierman RL Strausberg CM Fraser S Zhao J Shetty L Hou A Delcher B Zhu K Osoegawa P de Jong Genome Research, Vol. 14 (2004), pp. 1851-1860. 2007-12-25T07:44:55-00:00 2004 Genome Research 14 1851 1860 comparative-neuro evolution evolutionary-genomics evolvability genome-variation heredity systems-biology whole-genomic http://www.citeulike.org/user/balicea/article/2165124 <i>Journal of Biomedical Informatics, Vol. 35, No. 2. (2002), pp. 142-150.</i> Comparative genomics approaches to study organism similarities and differences. L Wei Y Liuc I Dubchakd J Shona J Park Journal of Biomedical Informatics, Vol. 35, No. 2. (2002), pp. 142-150. 2007-12-25T07:43:09-00:00 2002 Journal of Biomedical Informatics 35 2 142 150 comparative-neuro evolution evolutionary-genomics genome-variation heredity whole-genomic http://www.citeulike.org/user/balicea/article/2165120 <i>PNAS USA, Vol. 104, No. 18. (2007), pp. 7489-7494.</i> More genes underwent positive selection in chimpanzee evolution than in human evolution. MA Bakewell P Shi J Zhang PNAS USA, Vol. 104, No. 18. (2007), pp. 7489-7494. 2007-12-25T07:38:41-00:00 2007 PNAS USA 104 18 7489 7494 comparative-neuro evolution evolutionary-genomics genome-variation nat-selection-tests whole-genomic http://www.citeulike.org/user/balicea/article/2143057 <i>Integrative and Comparative Biology, Vol. 47, No. 1. (2007), pp. 16-54.</i> Neuromechanics: an integrative approach for understanding motor control. K Nishikawa AA Biewener P Aerts AN Ahn HJ Chiel MA Daley TL Daniel RJ Full ME Hale TL Hedrick AK Lappin TR Nichols RD Quinn RA Satterlie B Szymik Integrative and Comparative Biology, Vol. 47, No. 1. (2007), pp. 16-54. 2007-12-18T22:52:05-00:00 2007 Integrative and Comparative Biology 47 1 16 54 animal-model brain-anatomy comparative-neuro control-theory evolution movement-science musculoskeletal_systems neuro-mechanics performance-augmentation http://www.citeulike.org/user/balicea/article/423522 <i>Brain Behav Evol, Vol. 59, No. 5-6. (2002), pp. 273-293.</i><br /><br />[Olfactory senses, convergence, adaptation, constraint, odorant binding protein, G protein-coupled receptor, sensory transduction, glomerulus] As we learn more about the neurobiology of olfaction, it is becoming increasingly clear that olfactory systems of animals in disparate phyla possess many striking features in common. Why? Do these features provide clues about the ways the nervous system processes olfactory information? This might be the case if these commonalities are convergent adaptations that serve similar functions, but similar features can be present in disparate animals for other reasons. For example, similar features may be present because of inheritance from a common ancestor (homology), may represent responses to similar constraints, or may be superficial or reflect strategies used by researchers studying the system. In this paper, I examine four examples of features of olfactory systems in members of different phyla: the presence of odorant binding proteins in the fluid overlying olfactory receptor neurons; the use of G protein-coupled receptors as odorant receptors; the use of a two-step pathway in the transduction of odorant signals; and the presence of glomerular neuropils in the first central target of the axons of olfactory receptor cells. I analyze data from nematodes, arthropods, molluscs, and vertebrates to investigate the phylogenetic distribution of these features, and to try to explain the presence of these features in disparate animals. Phylogenetic analyses indicate that these features are not homologous across phyla. Although these features are often interpreted as convergent adaptations, I find that alternative explanations are difficult to dismiss. In many cases, it seems that olfactory system features that are similar across phyla may reflect both responses to similar constraints and adaptations for similar tasks. Why are olfactory systems of different animals so similar? HL Eisthen Brain Behav Evol, Vol. 59, No. 5-6. (2002), pp. 273-293. 2005-12-06T17:09:31-00:00 2002 Brain Behav Evol 0006-8977 59 5-6 273 293 comparative-neuro evolution evolvability phylogeny sensory-systems http://www.citeulike.org/user/balicea/article/2086412 <i>Journal of Neuroscience, Vol. 24, No. 13. (2004), pp. 3152-3163.</i> Parallel FoxP1 and FoxP2 expression in songbird and human brain predicts functional interaction. I Teramitsu LC Kudo SE London DH Geschwind SA White Journal of Neuroscience, Vol. 24, No. 13. (2004), pp. 3152-3163. 2007-12-10T18:16:39-00:00 2004 Journal of Neuroscience 24 13 3152 3163 behavior brain-anatomy comparative-neuro event-detection evolution learning-and-memory molecular-signaling neuro-coding neuroethology regulatory-cascades http://www.citeulike.org/user/balicea/article/2086404 <i>Systematic Biology, Vol. 46, No. 3. (1997), pp. 537-553.</i> Trees within trees: genes and species, molecules and morphology. JJ Doyle Systematic Biology, Vol. 46, No. 3. (1997), pp. 537-553. 2007-12-10T18:14:55-00:00 1997 Systematic Biology 46 3 537 553 comparative-neuro evolution modeling-and-simulation nat-selection-tests phylogeny http://www.citeulike.org/user/balicea/article/706101 <i>J Biol Rhythms, Vol. 14, No. 1. (February 1999), pp. 4-10.</i><br /><br />There is growing evidence in support of the hypothesis that, in mammals, photoreceptive tasks are segregated into those associated with creating a detailed visual image of the environment and those involved in the photic regulation of temporal biology. The hypothesis that this segregation extends to the use of different photoreceptors remains unproven, but published reports from several mammalian species that circadian photoentrainment survives a degree of retinal degeneration sufficient to induce visual blindness suggest that this may be so. This has lead to speculation that mammals might employ a dedicated 'circadian photoreceptor' distinct from the rod and cone cells of the visual system. The location and nature of this putative circadian photoreceptor has become a matter of conjecture. The latest candidates to be put forward as potential circadian photopigments are the mammalian cryptochrome proteins (CRY1 and 2), putative vitamin-B2 based photopigments. To date, published experimental evidence falls short of a definitive demonstration that these proteins form the basis of circadian photoreception in mammals. Consequently, this review aims to assess their suitability for this task in light of what we know regarding the biology of the cyrptochromes and the nature of mammalian photoentrainment. Photoentrainment in mammals: a role for cryptochrome? RJ Lucas RG Foster doi:10.1177/074873099129000380 J Biol Rhythms, Vol. 14, No. 1. (February 1999), pp. 4-10. 2006-06-21T18:08:53-00:00 1999 J Biol Rhythms 0748-7304 14 1 4 10 biological-rhythms comparative-neuro neuro-chem http://www.citeulike.org/user/balicea/article/2045653 <i>Genome Research, Vol. 10.1101/gr.7113408doi: (2007)</i> The genome-wide determinants of human and chimpanzee microsatellite evolution YD Kelkar S Tyekucheva F Chiaromonte KD Makova Genome Research, Vol. 10.1101/gr.7113408doi: (2007) 2007-12-02T19:41:46-00:00 2007 Genome Research 10.1101/gr.7113408doi: comparative-neuro evolution evolutionary-genomics informatics whole-genomic http://www.citeulike.org/user/balicea/article/2045647 <i>Genome Research, Vol. 10.1101/gr.6775107 doi: (2007)</i> Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions L Gordon S Yang M Tran-Gyamfi D Baggott M Christensen A Hamilton R Crooijmans M Groenen S Lucas I Ovcharenko L Stubbs Genome Research, Vol. 10.1101/gr.6775107 doi: (2007) 2007-12-02T19:39:20-00:00 2007 Genome Research 10.1101/gr.6775107 doi: comparative-neuro evo-devo evolution evolutionary-genomics informatics whole-genomic http://www.citeulike.org/user/balicea/article/1952168 <i>Nature Reviews Neuroscience, Vol. 8 (2007), 961.</i><br /><br />Charles Darwin appreciated the conceptual difficulty in accepting that an organ as wonderful as the vertebrate eye could have evolved through natural selection. He reasoned that if appropriate gradations could be found that were useful to the animal and were inherited, then the apparent difficulty would be overcome. Here, we review a wide range of findings that capture glimpses of the gradations that appear to have occurred during eye evolution, and provide a scenario for the unseen steps that have led to the emergence of the vertebrate eye. Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. TD Lamb SP Collin EN Pugh Nature Reviews Neuroscience, Vol. 8 (2007), 961. 2007-11-21T14:10:57-00:00 2007 Nature Reviews Neuroscience 8 961 brain-anatomy comparative-neuro evolution evolution-of-intelligence neuro-evolution http://www.citeulike.org/user/balicea/article/1943739 <i>Journal of Experimental Biology, Vol. 208 (2005), pp. 1665-1676.</i><br /><br />To function over a lifetime of use, materials and structures must be designed to have sufficient factors of safety to avoid failure. Vertebrates are generally built from materials having similar properties. Safety factors are most commonly calculated based on the ratio of a structure’s failure stress to its peak operating stress. However, yield stress is a more likely limit, and work of fracture relative to energy absorption is likely the most relevant measure of a structure’s safety factor, particularly under impact loading conditions characteristic of locomotion. Yet, it is also the most difficult to obtain. For repeated loading, fatigue damage and eventual failure may be critical to the design of biological structures and will result in lower safety factors. Although area:volume scaling predicts that stresses will increase with size, interspecific comparisons of mammals and birds show that skeletal allometry is modest, with most groups scaling (ld0.89) closer to geometric similarity (isometry: ld1.0) than to elastic similarity (ld0.67) or stress similarity (ld0.5). To maintain similar peak bone and muscle stresses, terrestrial mammals change posture when running, with larger mammals becoming more erect. More erect limbs increases their limb muscle mechanical advantage (EMA) or ratio of ground impulse to muscle impulse (r/R=G/Fm). The increase in limb EMA with body weight (W0.25) allows larger mammals to match changes in bone and muscle area (W0.72–0.80) to changes in muscle force generating requirements (W0.75), keeping bone and muscle stresses fairly constant across a size range 0.04–300·kg. Above this size, extremely large mammals exhibit more pronounced skeletal allometry and reduced locomotor ability. Patterns of ontogenetic scaling during skeletal growth need not follow broader interspecific scaling patterns. Instead, negative allometric growth (becoming more slender) is often observed and may relate to maturation of the skeleton’s properties or the need for younger animals to move at faster speeds compared with adults. In contrast to bone and muscle stress patterns, selection for uniform safety factors in tendons does not appear to occur. In addition to providing elastic energy savings, tendons transmit force for control of motion of more distal limb segments. Their role in elastic savings requires that some tendons operate at high stresses (and strains), which compromises their safety factor. Other ‘low stress’ tendons have larger safety factors, indicating that their primary design is for stiffness to reduce the amount of stretch that their muscles must overcome when contracting to control movement. Biomechanical consequences of scaling. AA Biewener Journal of Experimental Biology, Vol. 208 (2005), pp. 1665-1676. 2007-11-20T15:41:57-00:00 2005 Journal of Experimental Biology 208 1665 1676 adaptive-systems animal-model biological-inspired-modeling comparative-neuro movement-science musculoskeletal_systems neuro-mechanics http://www.citeulike.org/user/balicea/article/1903344 <i>PNAS USA, Vol. 103, No. 21. (2006), 8006.</i> Hotspots for copy number variation in chimps and humans. GH Perry PNAS USA, Vol. 103, No. 21. (2006), 8006. 2007-11-12T16:58:23-00:00 2006 PNAS USA 103 21 8006 comparative-neuro evolution evolutionary-genomics evolvability heredity whole-genomic http://www.citeulike.org/user/balicea/article/1815484 <i>PLoS Biology, Vol. 2, No. 7. (2004), 0937.</i> Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution A Fortna Y Kim E Maclaren K Marshall G Hahn L Meltesen M Brenton R Hink S Burgers T Hernandez-Boussard A Karimpour-Fard D Glueck L Mcgavran R Berry J Pollack JM Sikela PLoS Biology, Vol. 2, No. 7. (2004), 0937. 2007-10-24T13:57:30-00:00 2004 PLoS Biology 2 7 0937 comparative-neuro evolutionary-genomics phylogeny http://www.citeulike.org/user/balicea/article/1815428 <i>PLoS Biology, Vol. 2, No. 7. (2004), 0924.</i> Migratory Sleeplessness in the White-Crowned Sparrow (Zonotrichia leucophrys gambelii) NC Rattenborg BH Mandt WH Obermeyer PJ Winsauer R Huber M Wikelski RM Benca PLoS Biology, Vol. 2, No. 7. (2004), 0924. 2007-10-24T13:37:03-00:00 2004 PLoS Biology 2 7 0924 behavior brain-anatomy comparative-neuro sleep