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Human neuromaturation, juvenile extreme energy liability, and adult cognition/cooperation Nature Precedings
John Skoyles.
Human childhood and adolescence is the period in which adult cognitive competences (including those that create the unique cooperativeness of humans) are acquired. It is also a period when neural development puts a juvenile’s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses ≈50% of its total energy expenditure (TEE) (cf. adult ≈12%). This brain expensiveness is due to (1) the brain making up ≈6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is ≈100% greater in the gray matter of a child than in an adult (a result of the extra costs of synaptic neuromaturation). The high absolute number of...
Tipo: Manuscript Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7096/version/1
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Precise Similarity of Many Human Proteins to Proteins of Prokarya Nature Precedings
Roy Britten.
	 Proteins originated in early forms of life and have long survived, because they have always been required. Some recognizably similar proteins are found in all sequence comparisons between species, no matter how distant, including prokaryotes and eukaryotes. Reported here are observations on the relationships of human proteins to the proteins of 458 prokaryotes for which protein libraries are available. Each of these libraries includes a protein that matches a human protein with a BLAST score of 573 or more, indicating excellent conservation of certain amino acid sequences. A majority of these proteins also match a yeast protein and other eukaryote proteins with comparable accuracy, indicating that protein conservation is responsible in most...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/800/version/1
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A Quantitative Approach to Investigating the Hypothesis of Prokaryotic Intron Loss Nature Precedings
Robert M. Sinclair.
Using a novel method, we show that ordered triplets of motifs usually associated with spliceosomal intron recognition are underrepresented in the protein coding sequence of complete Thermotogae, archaeal and bacterial genomes. The underrepresentation observed does not extend to the noncoding strand, suggesting that the cause of the asymmetry is related to mRNA rather than DNA. Our data do not suggest that the underrepresentation is due to gene transfer from eukaryotes. We speculate that one possible explanation for these observations is that the protein coding sequence of Thermotogae, Archaea and Bacteria was at some time in the past subjected to selection against certain motifs appearing in an order which might initiate splicing in environments harboring...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5770/version/1
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Evolution of malaria virulence in cross-generation transmission through selective immune pressure Nature Precedings
David E. Gurarie.
Theoretical arguments and some mathematical models of host-parasite coevolution (e.g. [1- 6]) suggest host immunity as the driving source for the evolution of parasite virulence. Imperfect vaccines in particular, can play the role and recent work [7] sets to test these ideas experimentally, using the mouse malaria model, Plasmodium chabaudi. To this end the authors evolve parasite lines in immunized and nonimmunized (“naïve”) mice using serial passage of infected blood samples. They find parasite lines evolved in immunized mice become more virulent than those evolved in naive mice. Furthermore, this feature persisted even when the evolved strains were transmitted through mosquitoes. 
Here we develop a...
Tipo: Manuscript Palavras-chave: Immunology; Bioinformatics; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/203/version/1
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Cancer and the social induction of aging Nature Precedings
Rodrick Wallace; Deborah Wallace.
Age has long been known as the primary population 'risk factor' for cancer. We suggest that the observed disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be effectively addressed by 'small molecule' interventions at the individual level, but must involve comprehensive prevention...
Tipo: Manuscript Palavras-chave: Cancer; Immunology; Pharmacology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6146/version/1
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Early Life Relict Feature in Peptide Mass Distribution Nature Precedings
Roman A. Zubarev; Konstantin Artemenko; Alexander R. Zubarev; Corina Mayrhofer; Eva Y. M. Fung.
Molecular mass of a biomolecule is characterized in mass spectroscopy by the monoisitopic mass M~mono~ and the average isotopic mass M~av~. We found that peptide masses mapped on a plane made by two parameters derived from M~mono~ and M~av~ form a peculiar global feature in form of a band-gap 5-7 ppm wide stretching across the whole peptide galaxy, with a narrow (FWHM 0.2 ppm) line in the centre. The a priori probability of such a feature to emerge by chance is less than 1:100. Peptides contributing to the central line have elemental compositions following the rules S=0; Z = (2C - N - H)/2 =0, which nine out of 20 amino acid residues satisfy. The relative abundances of amino acids in the peptides contributing to the central line correlate with the...
Tipo: Manuscript Palavras-chave: Chemistry; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2402/version/1
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Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species Nature Precedings
Daniel Mietchen; Robert Dahnke; Christian Gaser.
INTRODUCTION

MR techniques have delivered images of brains from a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen & Dierker, 2007), which also hampers a deeper understanding of the mechanisms behind structural alterations in neurodevelopmental disorders (Kochunov et al., 2010). One of the reasons for this is the lack of computational tools suitable for morphometrci comparisons across multiple species. In this work, we aim to characterize this gap, taking primates as an...
Tipo: Poster Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4511/version/2
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Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents Nature Precedings
Anthonie W. J. Muller.
Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^ thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to macroscopic due to the selective advantage of a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3333/version/2
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Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_ Nature Precedings
Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3593/version/2
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The study of the umbilical system in planktonic foraminifera in relation with depth of the Abderaz Formation at type section, IRAN Nature Precedings
Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad.
Prospect of changes in such umbilical structures as Lip, Portici and Tegilla throughout Turonian-Campanian was also investigated. The phylogenic trend show that Lip structure in primary morphogroups turns gradually to tegilla in more developed forms in which the opening become also entirely umbilical. Statistical an analysis showed that the trends of changes are correlatable with increase in water depth while a decrease in depth result in development of lip in the planktonic foraminifera studied. The changes are considered to be in accord with Pascal law.
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3206/version/1
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Systema Naturae. Classification of living things. Nature Precedings
Alexey Shipunov.
Original classification of living organisms containing four kingdoms (Monera, Protista, Vegetabilia and Animalia), 60 phyla and 254 classes, is presented. The classification is based on latest available information.
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/241/version/2
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A Rate Distortion approach to protein symmetry Nature Precedings
Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein 'molten globule'. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty's (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript Palavras-chave: Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4280/version/1
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Subtyping of Dengue Viruses using Return Time Distribution based Appproach Nature Precedings
Pandurang Kolekar; Mohan Kale; Urmila Kulkarni-Kale.
Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided into respective genotypes. The association between DENV subtypes and the kind & severity of disease caused by them is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally intensive. Hence, the need for...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5590/version/1
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Evolution of Thriftiness: An analytical viewpoint Nature Precedings
Prajakta Belsare; Milind Watve.
We examine here, using a simple mathematical model, the conditions under which thrifty genes or fetal programming could evolve. Obesity and related disorders are thought to have their roots in metabolic thirftiness that evolved to combat periodic starvation. The failure to detect any thrifty genes and the association of low birth weight with type 2 diabetes, caused a shift in the concept from thrifty gene to thrifty phenotype and fetal programming. This hypothesis assumes that intra-uterine undernutrition programs the body to be thrifty, predicting and preparing for starvation in later life. However, there are reproductive costs associated with thriftiness. Results of the model suggest that under no condition thrifty and non-thrifty genes would co-exist...
Tipo: Poster Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2709/version/1
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The joys and perils of recombination - The hotspot conversion paradox and the evolution of recombination Nature Precedings
Mario Pineda-Krch; Rosemary J. Redfield.
The contradiction between the long-term persistence of the chromosomal hotspots that initiate meiotic recombination and the self-destructive mechanism by which they act strongly suggests that our understanding of recombination is incomplete. To investigate the requirements for hotspot persistence, Rosemary Redfield and I developed a computer simulation model, hotspot, of their activity and its evolutionary consequences.
Tipo: Presentation Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3636/version/1
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Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers Nature Precedings
Shi Huang.
Interpretations of molecular data by the modern evolution theory are often sharply inconsistent with paleontological results. This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution. The maximum genetic diversity (MGD) hypothesis is a more coherent and complete account of evolution that has yet to meet a single contradiction. Here, molecular data were analyzed based on the MGD to resolve key questions of primate phylogeny. A new method was developed from a novel result predicted by the MGD: genetic non-equidistance to a simpler taxon only in slow but not in fast evolving sequences given non-equidistance in time. This ‘slow clock’ method showed that humans are...
Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3794/version/1
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A new phylogenetic comparative method: detecting niches and transitions with continuous characters Nature Precedings
Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present examples of these weaknesses using a classic data set on Anoles lizards. I describe a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Presentation Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4615/version/1
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Exploring The Hidden Realms Of Global Biodiversity: Interesting Endophytic Yeast Flora From Floral Ovaries Nature Precedings
Nandkumar Kamat; Shweta S. Saudagar.
Soil is considered the ultimate reservoir of all the microbiota and specifically the yeasts. However their association with different plant organs and at different developmental stages is not fully explored. Although about 1000 yeast species have been identified, exploration of various microhabitats such as plant storage organs, flowers, nectar, and tree sap is expected to yield a large number of novel species, including interesting endophytic yeasts(Carlos & Gabor, 2006). Angiosperms are considered the most diverse group of the plant kingdom comprising of about 250,000 species (Kenrick, 1999). As part of an exhaustive exploration of yeasts associated with angiosperm flowers, specific attention was paid to floral ovaries to detect the presence of...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics & Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6268/version/1
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Essay: On the close relationship between speciation, inbreeding and recessive mutations. Nature Precedings
Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5003/version/2
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Copyrights and digitizing the systematic literature: the horror... the horror... Nature Precedings
N. Dean Pentcheff.
It is time for us to take full advantage of the investment that our societies have made in documenting the biodiversity of the world. It is time for us to fully, and legally, make systematic literature available worldwide. Using U.S. "Fair Use" guidelines, we can.
Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4644/version/1
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