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1 online resource (15 p.) : digital, PDF file.
This project has demonstrated the level of commercial readiness for production of the industrial chemical, 1,4-butanediol (BDO), from lignocellulosic biomass by engineered E. coli. Targets were BDO titer, rate, and yield (TRY) and growth in lignocellulosic hydrolysates (Hz). A range of Hzs were used to assess limitations for biomass-to-BDO. Via adaptive evolution methods, whole-genome sequencing, and introduction of identified target genes, strains co-utilizing C5/ C6 sugars were made. The composition of Hz versus TRY led to a modified Hz composition. This was used in partnership with the DOE to redirect the project to focus on 1) several biomass Hz from new suppliers, 2) Hz specification due to the characteristics of the Genomatica BDO process, 3) a gene cassette to engineer any BDO producing strain for biomass, and 4) modified BDO recovery to more economically recover BDO at industry specifications. BDO TRY and growth of the E. coli strains were predictable based on Hz composition from several suppliers. This defined metrics for biomass Hz composition to achieve BDO TRY along with internal TEA to evaluate the economic potential of each modification to strain, Hz feed, and process. An improved biomass-to-BDO production strain reached BDO T-R in a 30 L fermentation above original objectives. Yield approached the proposed Y and modifications to BDO recovery were demonstrated. Genomatica is now in the position of being able to incorporate biomass feedstocks into the commercial GENO BDO process.
1 online resource.
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1 online resource.
EBSCOhost Access limited to 1 user
1 online resource ( xxiii, 333 pages) :
  • Forward Part I: History of Attitudes toward Evolution in the South 1. Darwinism in the American South 2. Race and Evolution in Antebellum Alabama: The Polygenist Prehistory We'd Rather Ignore 3. "The Cadillac of Disclaimers": Twenty Years of Official Antievolution in Alabama4. Deconstructing the Alabama Disclaimer with Students: A Powerful Lesson in Evolution, Politics, and Persuasion Part II: Culture and Education in the American South 5. Evolution Acceptance among Preservice Science Teachers in the South6. Evolution Acceptance among Undergraduates in the South 7. Religion, Politics, and Science for U.S. Southerners 8. Sharing News and Views about Evolution in Social Media Part III: Perspectives and Resources from the Natural Sciences 9. Resources for Teaching Biological Evolution in the Deep South 10. Teaching Louisiana Students about Evolution by Comparing the Anatomy of Fishes and Humans 11. Teaching Evolution in Real Time 12. Trace Fossils of Alabama: Life in the Coal Age Part IV: Perspectives and Resources from the Social Sciences 13. What Can the Alabama Mississippians Teach Us about Human Evolution and Behavior?14. Tattooing Commitment, Quality, and Football in Southeastern North America APPENDIX: Additional Resources for Biological Evolution Education in Alabama Afterward.
  • (source: Nielsen Book Data)9781349951383 20170502
This volume reaches beyond the controversy surrounding the teaching and learning of evolution in the United States, specifically in regard to the culture, politics, and beliefs found in the Southeast. The editors argue that despite a deep history of conflict in the region surrounding evolution, there is a wealth of evolution research taking place-from biodiversity in species to cultural evolution and human development. In fact, scientists, educators, and researchers from around the United States have found their niche in the South, where biodiversity is high, culture runs deep, and the pace is just a little bit slower.
(source: Nielsen Book Data)9781349951383 20170502
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1 online resource.
  • Evolution in the dark - introduction.- The role of rudimentation in evolution.- Diversity and phylogenetic age of cave species.- Surface and cave populations of Mexican Astyanax.- Complexity of interrelationship of cave and surface fish.- Regressive and constructive traits in Astyanax surface and cave fish.- Mechanisms of regressive evolution.
  • (source: Nielsen Book Data)9783662545102 20170731
This book provides fascinating insights into the development and genetics of evolutionary processes on the basis of animals living in the dark, such as the Astyanax cave fish. Biologically functionless traits show high variability, which results from neutral deleterious mutations no longer being eliminated by natural selection, which normally acts to preserve functional capability. These negative mutations accumulate until the traits they are responsible for become rudimentary or even lost. The random genetic basis of regressive evolution is in accordance with Nei's Neutral Theory of Molecular Evolution, which applies to the molecular level. Such processes are particularly conspicuous in species living in constant darkness, where, for example in Astyanax, all traits depending on the exposure to light, like eyes, pigmentation, visually triggered aggressive behaviour, negative phototaxis, and several peripheral outcomes of circadian rhythmicity, are useless and diminish. In compensation constructive traits like taste, olfaction or the lateral line senses are improved by selection and do not show variability. Regressive and constructive traits inherit independently, proving that the rudimentation process is not driven by pleiotropic linkage between them. All these traits are subject to mosaic evolution and exhibit unproportional epistatic gene effects, which play an important role in evolutionary adaptation and improvement. Offering valuable evolutionary insights and supplemented by a wealth of illustrations, this book will appeal to evolutionary and developmental biologists alike.
(source: Nielsen Book Data)9783662545102 20170731
EBSCOhost Access limited to 1 user
1 online resource (1 streaming video file (44 min.) : color, sound).
  • Contents: Human evolutionary history
  • Human evolution and childbirth
  • Birth in other primates
  • How anatomical changes for bipedalism impact birth
  • Birth in early human ancestors
  • The helpless human newborn
  • The evolutionary legacy of birth
  • Why women benefit from assistance at birth
  • Value of emotional support during labor and delivery.
1 online resource ( xiii, 380 pages) :
  • Preface xi Chapter 1 Genes: How they are inherited 1 Blood and ABO blood groups 1 Inheritance of ABO blood groups 3 Inheritance of more than one gene: ABO and rhesus blood groups 4 Sex chromosomes 9 Determining how traits are inherited: Pedigree analysis 10 What is and isn t inherited 12 Concluding remarks 14 Chapter 2 What genes are, what they do, and how they do it 15 Chromosomes, proteins, and nucleic acids: Figuring out what genes are 15 The structure of genes and what they do: The central dogma and the flow of information 18 How genes do what they do: Transcription and translation 19 The genetic code 22 DNA replication 23 The consequences of mutations 23 What causes mutations? 25 A final cautionary note 26 Chapter 3 Genes in populations 27 What is a population? 27 The concept of effective population size 28 The sex ratio and Ne 29 Inbreeding and Ne 30 Variation in population size over time and Ne 30 Differential fertility and Ne 31 Ne for humans 33 Chapter 4 A simple model: Hardy Weinberg equilibrium 35 The gene pool with no evolution: The Hardy Weinberg principle 35 Exceptions 38 A real-life example 39 Some practical uses for Hardy Weinberg 41 Chapter 5 Evolutionary forces 45 Non random mating 45 Small population size 48 Mutation 53 Migration 56 Selection 60 Evolutionary forces: Summary 68 Chapter 6 Molecular evolution 69 Functionally less important molecules (or parts of molecules) evolve faster than more important ones 70 Conservative substitutions occur more frequently than disruptive ones 71 The rate of molecular evolution is approximately constant 72 Contrasting phenotypic and molecular evolution 73 How do new gene functions arise? 74 Gene regulation and phenotypic evolution 77 Chapter 7 Genetic markers 79 Classical markers: Immunogenetic markers 79 Classical markers: Biochemical polymorphisms 81 The first DNA markers: Restriction fragment length polymorphisms 84 Polymerase chain reaction 86 DNA sequencing: The sanger method 89 Next-generation sequencing 90 Targeting single DNA bases: SNPs 92 Variation in length 94 Other structural variation 99 Concluding remarks 100 Chapter 8 Sampling populations and individuals 103 Sampling populations: General issues 103 Sampling populations: Ethical issues 105 Archival samples 108 Chapter 9 Sampling DNA regions 111 Mitochondrial DNA 111 Y chromosomal DNA 116 Autosomal DNA 119 X chromosome DNA 121 Public databases 122 Chapter 10 Analysis of genetic data from populations 125 Genetic diversity within populations 125 Genetic distances between populations 128 Displaying genetic distance data: Trees 135 Displaying genetic data: Multidimensional scaling, principal components, and correspondence analysis 139 Chapter 11 Analysis of genetic data from individuals 147 Genetic distances for DNA sequences 147 Trees for DNA sequences 153 Rooting trees 156 Assessing the confidence of a tree 157 Network analyses 160 Genome-wide data: Unsupervised analyses 161 Chapter 12 Inferences about demographic history 175 Dating events 175 Population size and population size change 187 Migration and admixture 194 Putting it all together 197 Chapter 13 Our closest living relatives 201 Resolving the trichotomy 205 Complications 206 Ape genetics and genomics 208 Chapter 14 The origins of our species 211 Human origins: The fossil record 215 Models for human origins 218 The genetic evidence: mtDNA 222 The genetic evidence: Y chromosome 224 The genetic evidence: Autosomes 225 Chapter 15 Ancient DNA 229 Properties of ancient DNA: Degradation 229 Properties of ancient DNA: Damage 229 Properties of ancient DNA: Contamination 232 History of ancient DNA studies 236 Ancient DNA: Archaic humans 237 Other uses for ancient DNA 244 Chapter 16 Dispersal and migration 247 Out of Africa how many times, when, and which way did they go? 251 Into remote lands: The colonization of the Americas 259 Into even more remote lands: The colonization of Polynesia 267 Some concluding remarks 281 Chapter 17 Species-wide selection 283 Species-wide selection 284 Nonsynonymous mutations and the dN/dS ratio 284 Tests based on the allele frequency distribution 288 Selection tests based on comparing divergence to polymorphism 293 Archaic genomes 297 Chapter 18 Local selection 299 Example: Lactase persistence 304 Example: EDAR 309 Ancient DNA 318 Concluding remarks 318 Chapter 19 Genes and culture 321 Are humans still evolving? 321 Genetic variation can be directly influenced by cultural practices 322 Genetic variation can be indirectly influenced by cultural practices 322 Using genetic analyses to learn more about cultural practices: Agricultural expansions 326 Using genetic analyses to learn more about cultural practices: Language replacements 332 Using genetic analyses to learn more about cultural practices: Dating the origin of clothing 333 Concluding remarks 339 Chapter 20 Ongoing and future developments in molecular anthropology 341 More and different kinds of data: The other omics 341 Beyond you : The microbiome 344 More analyses 347 Relating phenotypes to genotypes 351 Personal ancestry testing and genomics 360 References 363 Suggestions for additional reading 373 Index 375.
  • (source: Nielsen Book Data)9781118061626 20170502
Molecular anthropology uses molecular genetic methods to address questions and issues of anthropological interest. More specifically, molecular anthropology is concerned with genetic evidence concerning human origins, migrations, and population relationships, including related topics such as the role of recent natural selection in human population differentiation, or the impact of particular social systems on patterns of human genetic variation. Organized into three major sections, An Introduction to Molecular Anthropology first covers the basics of genetics what genes are, what they do, and how they do it as well as how genes behave in populations and how evolution influences them. The following section provides an overview of the different kinds of genetic variation in humans, and how this variation is analyzed and used to make evolutionary inferences. The third section concludes with a presentation of the current state of genetic evidence for human origins, the spread of humans around the world, the role of selection and adaptation in human evolution, and the impact of culture on human genetic variation. A final, concluding chapter discusses various aspects of molecular anthropology in the genomics era, including personal ancestry testing and personal genomics. An Introduction to Molecular Anthropology is an invaluable resource for students studying human evolution, biological anthropology, or molecular anthropology, as well as a reference for anthropologists and anyone else interested in the genetic history of humans.
(source: Nielsen Book Data)9781118061626 20170502
EBSCOhost Access limited to 3 simultaneous users
1 online resource (p. 1-5 ): digital, PDF file.
Ni<sub>x</sub>WO<sub>2.72</sub> nanorods (NRs) are synthesized by a one-pot reaction of Ni(acac)<sub>2</sub> and WCl<sub>4</sub>. In the rod structure, Ni(II) intercalates in the defective perovskite-type WO<sub>2.72</sub> and is stabilized. The Ni<sub>x</sub>WO<sub>2.72</sub> NRs show the x-dependent electrocatalysis for the oxygen evolution reaction (OER) in 0.1M KOH with Ni<sub>0.78</sub>WO<sub>2.72</sub> being the most efficient, even outperforming the commercial Ir-catalyst. Lastly, the synthesis is not limited to Ni<sub>x</sub>WO<sub>2.72</sub> but can be extended to M<sub>x</sub>WO<sub>2.72</sub> (M = Co, Fe) as well, providing a new class of oxide-based catalysts for efficient OER and other energy conversion reactions.
1 online resource (1 streaming video file (32 min.) : color, sound).
  • Contents: Defining menopause
  • Cross-species comparisons in length of post-reproductive life
  • Menopause and post-reproductive life in hominin evolution
  • Hypotheses to explain evolution of menopause and post-reproductive life.
1 online resource (53 p.) : digital, PDF file.
The implosion phase for Inertial Confinement Fusion (ICF) occurs from initiation of the drive until just before stagnation. Evolution of the shell and fusion fuel during the implosion phase is affected by the initial conditions of the target, the drive history. Poor performing implosions are a result of the behavior that occurs during the implosion phase such as low mode asymmetries, mixing of the ablator into the fuel, and the hydrodynamic evolution of initial target features and defects such as the shell mounting hardware. The ultimate results of these effects can only be measured at stagnation. However, studying the implosion phase can be effective for understanding and mitigating these effects and for of ultimately improving the performance of ICF implosions. As the ICF program moves towards the 2020 milestone to “determine the efficacy of ignition”, it will be important to understand the physics that occurs during the implosion phase. This will require both focused and integrated experiments. Focused experiments will provide the understanding and the evidence needed to support any determination concerning the efficacy of ignition.
Article No. 221 : digital, PDF file.
Species and phylogenetic lineages have evolved to differ in the way that they acquire and deploy resources, with consequences for their physiological, chemical and structural attributes, many of which can be detected using spectral reflectance form leaves. Recent technological advances for assessing optical properties of plants offer opportunities to detect functional traits of organisms and differentiate levels of biological organization across the tree of life. We connect leaf-level full range spectral data (400–2400 nm) of leaves to the hierarchical organization of plant diversity within the oak genus (Quercus) using field and greenhouse experiments in which environmental factors and plant age are controlled. We show that spectral data significantly differentiate populations within a species and that spectral similarity is significantly associated with phylogenetic similarity among species. Furthermore, we show that hyperspectral information allows more accurate classification of taxa than spectrally-derived traits, which by definition are of lower dimensionality. Finally, model accuracy increases at higher levels in the hierarchical organization of plant diversity, such that we are able to better distinguish clades than species or populations. This pattern supports an evolutionary explanation for the degree of optical differentiation among plants and demonstrates potential for remote detection of genetic and phylogenetic diversity.
1 online resource (1 streaming video file (48 min.) : color, sound).
  • Contents: Biodemography of lifespan: concepts, lifespan and sociality, and human lifespan evolution
  • Population biology of the elderly: role of elderly in nature & emphasis on social species
  • Experimental biodemography of aging: studies in model organisms.
1 online resource (1 streaming video file (24 min.) : color, sound).
  • Contents: Uniformitarianism, Lamarckism and Darwin's theory
  • Mendel’s work and the science of genetics
  • The modern synthesis: a mechanistic basis for variation and heredity
  • Molecular biology: the age of biological information
  • Rethinking gradual progressive evolution
  • Evolutionary biology in the age of genomics
  • Eugenics, the dark chapter of evolutionary biology
  • Group-level selection and evolution of morality.
1 online resource (1 streaming video file (8 min.) : color, sound).
  • Contents: Simplification of structure and function as reverse evolution
  • Chronic diseases & pathologies in different tissues and organs
  • Breakdown in cell-cell communication
  • Fibrosis & PPARγ agonists
  • Sensing loss of homeostasis & cellular perturbations.
1 online resource ( 1 PDF 38 pages) : illustrations.
  • 1. The origins of new mutations
  • 2. The origins of new species
  • Large scale genome changes
  • Clinical whole genome changes
  • Genome duplication and speciation
  • Ethical, legal, social implications: the safety of GMOs
  • 3. Evolution of allergic responses
  • Ethical, legal, social implications: balancing the rights of the individual vs. the group
  • Conclusion
  • Glossary
  • Index.
Once the first cell arose on Earth, how did genetic diversity arise if DNA replication and cell division generate exact copies? The answer is that neither process is perfect and that changes do occur at each step. Some changes are small and subtle while others are large and dramatic. As DNA mutates, evolution of a population takes place. But when can someone determine if a single species has changed enough to be considered two separate species? How is a species defined and is this definition useful in the real world? Real biological data will be examined to confront and answer these questions. Finally, the book examines an example of evolution that takes place in humans on a regular basis-the mammalian immune system. White blood cells evolve rapidly to confront any substance that enters a body and is perceived as a threat. With each exposure, these cells get better and better at neutralizing the threat.".
(source: Nielsen Book Data)9781606509876 20170821
1 online resource (1 streaming video file (16 min.) : color, sound).
  • Contents: Niche construction: definitions and examples
  • The endomembrane system
  • Advent of cholesterol depended on oxygen
  • Ecosystems and the process of death
  • Internal niche construction
  • The swim-bladder, the lung and PTHrP
  • Niche construction and epigenetics interactions
  • Gaia hypothesis.
1 online resource (38 p.) : digital, PDF file.
Here, we compare evolutionary predictions of double compact object merger rate densities with initial and forthcoming LIGO/Virgo upper limits. We find that: (i) Due to the cosmological reach of advanced detectors, current conversion methods of population synthesis predictions into merger rate densities are insufficient. (ii) Our optimistic models are a factor of 18 below the initial LIGO/Virgo upper limits for BH–BH systems, indicating that a modest increase in observational sensitivity (by a factor of ~2.5) may bring the first detections or first gravitational wave constraints on binary evolution. (iii) Stellar-origin massive BH–BH mergers should dominate event rates in advanced LIGO/Virgo and can be detected out to redshift z sime 2 with templates including inspiral, merger, and ringdown. Normal stars ($\lt 150\; {M}_{\odot }$) can produce such mergers with total redshifted mass up to ${M}_{{\rm{tot, z}}}\simeq 400\; {M}_{\odot }$. (iv) High black hole (BH) natal kicks can severely limit the formation of massive BH–BH systems (both in isolated binary and in dynamical dense cluster evolution), and thus would eliminate detection of these systems even at full advanced LIGO/Virgo sensitivity. We find that low and high BH natal kicks are allowed by current observational electromagnetic constraints. (v) The majority of our models yield detections of all types of mergers (NS–NS, BH–NS, BH–BH) with advanced detectors. Numerous massive BH–BH merger detections will indicate small (if any) natal kicks for massive BHs.
1 online resource (20 p.) : digital, PDF file.
Here, sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % <i>S. officinarum</i>, 10-20 % <i>S. spontaneum</i>, and 10 % recombinants between these two species. Analysis of a genomic region in the progenitor autoploid genomes of sugarcane hybrid cultivars will reveal the nature and divergence of homologous chromosomes. As a result, to investigate the origin and evolution of haplotypes in the <i>Bru1</i> genomic regions in sugarcane cultivars, we identified two BAC clones from <i>S. spontaneum</i> and four from <i>S. officinarum</i> and compared to seven haplotype sequences from sugarcane hybrid R570. The results clarified the origin of seven homologous haplotypes in R570, four haplotypes originated from <i>S. officinarum</i>, two from <i>S. spontaneum</i> and one recombinant.. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence ranged from 18.2 % to 60.5 % with an average of 33. 7 %. Gene content and gene structure were relatively well conserved among the homologous haplotypes. Exon splitting occurred in haplotypes of the hybrid genome but not in its progenitor genomes. Tajima's D analysis revealed that <i>S. spontaneum</i> hapotypes in the Bru1 genomic regions were under strong directional selection. Numerous inversions, deletions, insertions and translocations were found between haplotypes within each genome. In conclusion, this is the first comparison among haplotypes of a modern sugarcane hybrid and its two progenitors. Tajima's D results emphasized the crucial role of this fungal disease resistance gene for enhancing the fitness of this species and indicating that the brown rust resistance gene in R570 is from <i>S. spontaneum</i>. Species-specific InDel, sequences similarity and phylogenetic analysis of homologous genes can be used for identifying the origin of <i>S. spontaneum</i> and <i>S. officinarum</i> haplotype in <i>Saccharum</i> hybrids. Comparison of exon splitting among the homologous haplotypes suggested that the genome rearrangements in <i>Saccharum</i> hybrids <i>S. officinarum</i> would be sufficient for proper genome assembly of this autopolyploid genome. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence may allow sequencing and assembling the autopolyploid <i>Saccharum</i> genomes and the auto-allopolyploid hybrid genomes using whole genome shotgun sequencing.
1 online resource (14 p. ) : digital, PDF file.
In this study, the toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. However, M. extorquens AM1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. Only a few studies have reported the general stress response of M. extorquens AM1 to solvent stress. Therefore, it is highly desirable to obtain a strain with ameliorated 1-butanol tolerance and elucidate the molecular mechanism of 1-butnaol tolerance in M. extorquens AM1 for future strain improvement. In this work, adaptive laboratory evolution was used as a tool to isolate mutants with 1-butanol tolerance up to 0.5 %. The evolved strains, BHBT3 and BHBT5, demonstrated increased growth rates and higher survival rates with the existence of 1-butanol. Whole genome sequencing revealed a SNP mutation at kefB in BHBT5, which was confirmed to be responsible for increasing 1-butanol tolerance through an allelic exchange experiment. Global metabolomic analysis further discovered that the pools of multiple key metabolites, including fatty acids, amino acids, and disaccharides, were increased in BHBT5 in response to 1-butanol stress. Additionally, the carotenoid synthesis pathway was significantly down-regulated in BHBT5. In conclusion, we successfully screened mutants resistant to 1-butanol and provided insights into the molecular mechanism of 1-butanol tolerance in M. extorquens AM1. This research will be useful for uncovering the mechanism of cellular response of M. extorquens AM1 to solvent stress, and will provide the genetic blueprint for the rational design of a strain of M. extorquens AM1 with increased 1-butanol tolerance in the future.
1 online resource (p. 138-147 ): digital, PDF file.
I present a very personalized journey through more than three decades of computing for experimental high-energy physics, pointing out the enduring lessons that I learned. This is followed by a vision of how the computing environment will evolve in the coming ten years and the technical challenges that this will bring. I then address the scale and cost of high-energy physics software and examine the many current and future challenges, particularly those of management, funding and software-lifecycle management. Lastly, I describe recent developments aimed at improving the overall coherence of high-energy physics software.