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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 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.
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.
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.
p. 3420-3431 : digital, PDF file.
Cytosolic glutaminyl-tRNA synthetase (GlnRS) is the singular enzyme responsible for translation of glutamine codons. Compound heterozygous mutations in GlnRS cause severe brain disorders by a poorly understood mechanism. Herein, we present crystal structures of the wild type and two pathological mutants of human GlnRS, which reveal, for the first time, the domain organization of the intact enzyme and the structure of the functionally important N-terminal domain (NTD). Pathological mutations mapping in the NTD alter the domain structure, and decrease catalytic activity and stability of GlnRS, whereas missense mutations in the catalytic domain induce misfolding of the enzyme. Our results suggest that the reduced catalytic efficiency and a propensity of GlnRS mutants to misfold trigger the disease development. As a result, this report broadens the spectrum of brain pathologies elicited by protein misfolding and provides a paradigm for understanding the role of mutations in aminoacyl-tRNA synthetases in neurological diseases. Keywords
1 online resource (1 streaming video file (11 min.) : color, sound).
  • Contents: History of descriptive physiology
  • Systems biology
  • The biota expansion
  • Downward causation vs. cell-cell signaling
  • Holism vs. Reductionism: philosophical views about nature
  • Molecular changes mediating evolution
  • Cell communication as mechanism of novelty
  • From phylogeny-ontogeny to homeostasis & repair
  • Homeostasis as the mechanism for evolution
  • Explicate/Implicate order.
1 online resource (1 streaming video file (31 min.) : color, sound).
  • Contents: Developmental plasticity
  • Genes and environment in development
  • Adaptive developmental decisions and their betrayal if conditions change
  • Phenotypic accommodation
  • Multiple pathways
  • Myth of single gene control
  • Blueprints and programs as false metaphors
  • Cross-generational continuity of the phenotype
  • Origins of novel phenotypes including disease.
1 streaming video (141 minutes) : sound, colour.
  • Section 1. Differential evolution
  • Lesson 1. Explaining differential evolution
  • Lesson 2. Improvements to differential evolution
  • Lesson 3. Benchmarks of differential evolution
  • Section 2. Application of DE to tree model reconstruction
  • Lesson 4. Procedural tree models in tree model reconstruction
  • Lesson 5. Automatic modeling of trees using differential evolution
  • Lesson 6. Reconstructing trees from images using differential evolution
  • Section 3. Application of differential evolution in underwater glider path planning
  • Lesson 7. Solving underwater robotics challenges with differential evolution
  • Lesson 8. Planning glider paths using differential evolution
  • Lesson 9. Differential evolution performance comparison
  • Section 4. Application of differential evolution in hydro and thermal power plant scheduling
  • Lesson 10. Hydro-thermal scheduling using differential evolution
  • Lesson 11. Parallel differential evolution
  • Lesson 12. Surrogate differential evolution
  • Section 5. Applications of differential evolution in real world industrial challenges
  • Lesson 13. CEC 2011 benchmarks of differential evolution
  • Lesson 14. Open issues of differential evolution
  • Lesson 15. Forthcoming challenges of differential evolution.
Differential Evolution (DE) is one of the most popular, high-performance optimization algorithms with variants that have been outperforming others for years. As a result, DE has grown to accommodate wide usage for a variety of disciplines across scientific fields. Differential Evolution and Large-Scale Optimization Applications presents a research-based overview and cross-disciplinary applications of optimization algorithms. Emphasizing applications of Differential Evolution (DE) across sectors and laying the foundation for further use of DE algorithms in real-world settings, this video is an essential resource for researchers, engineers, and graduate-level students.
Article No. e1002475 : digital, PDF file.
In this study, the evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in <i>Streptomyces</i>, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the <i>Streptomyces</i> genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in <i>Streptomyces</i>, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in <i>Streptomyces</i>, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic <i>Streptomyces</i> for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology.
1 online resource (1 streaming video file (15 min.) : color, sound).
  • Contents: Tissue interactions during morphogenesis
  • Automaturation due to mechanotransduction
  • PTHrP is stretch-regulated
  • Dissociation of endoderm from mesoderm and fibrosis
  • Co-culture of endoderm and mesoderm lead to homeostasis
  • Neutral Lipid Trafficking.
1 online resource (1 streaming video file (33 min.) : color, sound).
  • Contents: Evolution of endothermy
  • PTHrP, Glucocorticoid and β-Adrenergic Receptor gene duplications
  • Hypoxia integrates respiratory and endocrine systems
  • Selection pressure for integrated physiology: lung, kidney, heart
  • Ontogeny-phylogeny of lung cell evolution
  • Swim bladder-lung functional homology
  • PTHrP is stretch-regulated
  • Chemiosmosis-homeostasis and the origins of life
  • Vertical integration of the effect of cholesterol on homeostasis
  • Cell-cell interactions and adaptation to oxygen
  • Endothermy as exaptation of oxygen adaptation
  • Physiologic homology based on cell-cell interactions.
1 online resource.
  • Front Cover ; Fractional Evolution Equations and Inclusions ; Copyright ; Table of Contents ; Preface; Chapter 1: Preliminaries; 1.1 Basic Facts and Notation ; 1.2 Fractional Integrals and Derivatives
  • 1.3 Semigroups and Almost Sectorial Operators 1.4 Spaces of Asymptotically Periodic Functions ; 1.5 Weak Compactness of Sets and Operators
  • 1.6 Multivalued Analysis1.7 Stochastic Process; Chapter 2: Fractional Evolution Equations; 2.1 Cauchy Problems; 2.2 Bounded Solutions on Real Axis ; 2.3 Notes and Remarks ; Chapter 3: Fractional Evolution Inclusions With Hille-yosida Operators; 3.1 Existence of Integral Solutions
  • 3.2 Topological Structure of Solution Sets 3.3 Notes and Remarks ; Chapter 4: Fractional Control Systems ; 4.1 Existence and Optimal Control ; 4.2 Optimal Feedback Control; 4.3 Controllability; 4.4 Approximate Controllability
  • 4.5 Topological Structure of Solution Sets 4.6 Notes and Remarks ; Chapter 5: Fractional Stochastic Evolution Inclusions; 5.1 Existence of Mild Solutions
Fractional evolution inclusions are an important form of differential inclusions within nonlinear mathematical analysis. They are generalizations of the much more widely developed fractional evolution equations (such as time-fractional diffusion equations) seen through the lens of multivariate analysis. Compared to fractional evolution equations, research on the theory of fractional differential inclusions is however only in its initial stage of development. This is important because differential models with the fractional derivative providing an excellent instrument for the description of memory and hereditary properties, and have recently been proved valuable tools in the modeling of many physical phenomena. The fractional order models of real systems are always more adequate than the classical integer order models, since the description of some systems is more accurate when the fractional derivative is used. The advantages of fractional derivatization become evident in modeling mechanical and electrical properties of real materials, description of rheological properties of rocks and in various other fields. Such models are interesting for engineers and physicists as well as so-called pure mathematicians. Phenomena investigated in hybrid systems with dry friction, processes of controlled heat transfer, obstacle problems and others can be described with the help of various differential inclusions, both linear and nonlinear. Fractional Evolution Equations and Inclusions is devoted to a rapidly developing area of the research for fractional evolution equations & inclusions and their applications to control theory. It studies Cauchy problems for fractional evolution equations, and fractional evolution inclusions with Hille-Yosida operators. It discusses control problems for systems governed by fractional evolution equations. Finally it provides an investigation of fractional stochastic evolution inclusions in Hilbert spaces.
1 online resource (1 streaming video file (5 min.) : color, sound).
  • Contents: Basis for predictive medicine
  • Utility in rational drug design & improving medical practices
  • Bioethics based on physiologic principles
  • A universal database for the natural sciences
  • The ideal human living environment.
1 online resource (458 p.)
p. 1757-1766 : digital, PDF file.
The genome sequences of more than 100 strains of the yeast <i>Saccharomyces cerevisiae</i> have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of <i>S. cerevisiae</i> derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any <i>S. cerevisiae</i> strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. Lastly, the Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.