Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation

The angiosperm radiation has been linked to sharp declines in gymnosperm diversity and the virtual elimination of conifers from the tropics. The conifer family Podocarpaceae stands as an exception with highest species diversity in wet equatorial forests. It has been hypothesized that efficient light harvesting by the highly flattened leaves of several podocarp genera facilitates persistence with canopy-forming angiosperms, and the angiosperm ecological radiation may have preferentially favoured the diversification of these lineages. To test these ideas, we develop a molecular phylogeny for Podocarpaceae using Bayesian-relaxed clock methods incorporating fossil time constraints. We find several independent origins of flattened foliage types, and that these lineages have diversified predominantly through the Cenozoic and therefore among canopy-forming angiosperms. The onset of sustained foliage flattening podocarp diversification is coincident with a declining diversification rate of scale/needle-leaved lineages and also with ecological and climatic transformations linked to angiosperm foliar evolution. We demonstrate that climatic range evolution is contingent on the underlying state for leaf morphology. Taken together, our findings imply that as angiosperms came to dominate most terrestrial ecosystems, competitive interactions at the foliar level have profoundly shaped podocarp geography and as a consequence, rates of lineage diversification.     

Domestic Transitions, Desiccation, Agricultural Intensification, and Livelihood Diversification among Rural Households on the Central Plateau, Burkina Faso

ABSTRACT   Understanding how and why domestic groups alter their function and form has long been a theme within anthropology. Numerous accounts have detailed the processes that drive household transformations and their underlying mechanisms. Mostly, these studies describe how domestic groups fission and fuse between extended and nuclear forms. In recent years, scholars have emphasized that these transformations should be understood within larger contexts of social and environmental change. Mossi communities on the Central Plateau of Burkina Faso provide an excellent opportunity to explore such processes because the large extended households documented 30 years ago were predicted to decline and eventually disappear. In this study, I examine dynamics of household transformations and test the validity of this prediction. I use perspectives from sustainability science and computer-simulation modeling to understand how regional desiccation, agricultural intensification, and livelihood diversification articulate with domestic transitions.     

Structural Transformations of Ice at High Pressures Via Molecular Dynamics Simulations

Abstract

A simple classical model is used for the study of the structural transformations of ice under high pressures, such as ice VIII to VII and X, via classical molecular dynamics (MD) simulation. In the present MD simulation, pair potentials of a simple form between pair of atoms and a thee-body potential representing the H-O-H angle dependence, originally developed by Kawamura et al., were used. Starting with a stable ice VIII at low pressure and low temperature, we have carried out two different MD runs, one with increasing pressure keeping the temperature constant (simulation I) and the other with increasing temperature under constant pressure (simulation II). From these MD simulations we have obtained the structural transformations from ice VIII to VII for both simulations; the former was finally transformed into ice X for the simulation I. The present results are compatible with recent experiments on high pressure ices.     

Habitat use affects morphological diversification in dragon lizards

Habitat use may lead to variation in diversity among evolutionary lineages because habitats differ in the variety of ways they allow for species to make a living. Here, we show that structural habitats contribute to differential diversification of limb and body form in dragon lizards (Agamidae). Based on phylogenetic analysis and ancestral state reconstructions for 90 species, we find that multiple lineages have independently adopted each of four habitat use types: rock‐dwelling, terrestriality, semi‐arboreality and arboreality. Given these reconstructions, we fit models of evolution to species’ morphological trait values and find that rock‐dwelling and arboreality limit diversification relative to terrestriality and semi‐arboreality. Models preferred by Akaike information criterion infer slower rates of size and shape evolution in lineages inferred to occupy rocks and trees, and model‐averaged rate estimates are slowest for these habitat types. These results suggest that ground‐dwelling facilitates ecomorphological differentiation and that use of trees or rocks impedes diversification.     

The Potential Applications of Nanoporous Materials for the Adsorption,Separation, and Catalytic Conversion of Carbon Dioxide

Carbon capture and storage (CCS) technologies aiming at tackling CO₂ emission have attracted much attention from scientists of various backgrounds. Most CCS systems require an efficient adsorbent to remove CO₂ from sources such as fossil fuels (pre‐combustion) or flue gas from power generation (post‐combustion). Research on developing efficient adsorbents with a substantial capacity, good stability and recyclability has grown rapidly in the past decade. Because of their high surface area, highly porous structure, and high stability, various nanoporous materials have been viewed as good candidates for this challenging task. Here, recent developments in several classes of nanoporous materials, such as zeolites, metal organic frameworks (MOFs), mesoporous silicas, carbon nanotubes, and organic cage frameworks, for CCS are examined and potential future directions for CCS technology are discussed. The main criteria for a sustainable CO₂ adsorbent for industrial use are also rationalized. Moreover, catalytic transformations of CO₂ to other chemical species using nanoporous catalysts and their potential for large scale carbon capture and utilization (CCU) processes are also discussed. Application of CCU technologies avoids any potential hazard associated with CO₂ reservoirs and allows possible recovery of some running cost for CO₂ capture by manufacturing valuable chemicals.     

Structural chemoproteomics and drug discovery

Our laboratories have developed several technologies to accelerate drug discovery process on the basis of structural chemoproteomics. They include SPS technology for the efficient determination of protein structures, SCP technology for the rapid lead generation and SDF technology for the productive lead optimization. Using these technologies, we could determine many 3D structures of target proteins bound with biologically active chemicals including the structure of phosphodiesterase 5/Viagra complex and obtain highly potent compounds in animal models of obesity, diabetes, cancer and inflammation. In this paper, we will discuss concepts and applications of structural chemoproteomics for drug discovery.     

Molecular clocks: four decades of evolution

During the past four decades, the molecular-clock hypothesis has provided an invaluable tool for building evolutionary timescales, and has served as a null model for testing evolutionary and mutation rates in different species. Molecular clocks have also influenced the development of theories of molecular evolution. As DNA-sequencing technologies have progressed, the use of molecular clocks has increased, with a profound effect on our understanding of the temporal diversification of species and genomes.     

Examination of structural stability and phase transitions in constant-pressure first-principles molecular dynamics simulations

Constant-pressure first-principles molecular dynamics (FPMD) simulation is a powerful tool for investigations of structures in crystals. However, it needs enourmous computations so that highly accurate calculations for electronic states cannot be employed at present. In this report, we examined the reliability and applicability of constant-pressure FPMD in the study of structural properties under this limitation. Crystalline silicon was employed as a benchmark to perform constant-pressure FPMD simulations (with a deformable simulation cell). It is found that, in high pressure (metallic) phases, crystalline symmetry is broken with the present simulation conditions. Several structural transformations were realized by compression and decompression, but they are not entirely consistent with experiment. We discuss this discrepancy and conclude that the number of k point sampling in the Brillouin zone is crucial. It is recommended that constant-pressure FPMD is employed to explore candidate structures for unknown solid phases at present computational resources.     

High-throughput cell-free systems for synthesis of functionally active proteins

Continuous cell-free translation systems with perpetual supply of consumable substrates and removal of reaction products made the process of in vitro synthesis of individual proteins sustainable and productive. Improvements of cell-free reaction mixtures, including new ways for efficient energy generation, had an additional impact on progress in cell-free protein synthesis technology. The requirement for gene-product identification in genomic studies, the development of high-throughput structural proteomics, the need for protein engineering without cell constraints (including the use of unnatural amino acids), and the need to produce cytotoxic, poorly expressed and unstable proteins have caused increased interest in cell-free protein synthesis technologies for molecular biologists, biotechnologists and pharmacologists.     

Empirical comparison of distance equations using discrete traits

The use of the Grewal-Smith statistic in measuring biological distance among skeletal population samples has been questioned since it was first applied to human populations. Recently, in an attempt to stabilize the variance of the Grewal-Smith statistic for use with non-metric analysis, Sjøvold ('73) and Green and Suchey ('76) have introduced corrections and alternative transformations which may enhance the meaning of biological distance among population samples. Their recommendations improve the statistics for specific variable ranges; i.e., small sample size and low trait frequencies. Thirteen equations representing Grewal-Smith, Freeman-Tukey, Anscombe, and Bartlett transformations and/or corrections, were compared using rank order correlation statistics on actual biological distances generated by real population data as presented in existing literature. Results from testing these actual distance models show little variation between equations based on the populational data sets used. Based on these findings, the distance model resulting from the Grewal-Smith statistic is not inferior to the more sophisticated models, although the latter may be superior by allowing specific improvements for small sample size and/or low trait frequencies.     

The postparietal shield of the Pragian dipnomorph Arquatichthys and its implications for the rhipidistian cranial anatomy

Rhipidistians comprise dipnomorphs (the lungfish lineage) and tetrapodomorphs (the tetrapod lineage). Arquatichthys porosus Lu and Zhu, 2008 is a Pragian dipnomorph from the Posongchong Formation of Zhaotong, Yunnan, South China (∼409 million years ago, Early Devonian), previously represented by a lower jaw and few scattered scales. Here we describe a newly-discovered postparietal shield of Arquatichthys by means of high-resolution computed tomography. The cranial morphology of Arquatichthys resembles that of the basal dipnomorph Powichthys in having more than two supratemporal bones each side, more than one row of openings for sensory canals on the marginal bones, and a straight posterior margin of the shield. An intricate occipital artery system is present between the skull roof and neurocranium, as in Youngolepis and the tetrapodomorph Eusthenopteron. The discovery of the postparietal shield of Arquatichthys adds new evidence in the cranial evolution of rhipidistians, and helps to improve our understanding of the character transformations during the early diversification of rhipidistians.     

Mozzarella Cheese – A Review of the Structural Development During Processing

From its journey from milk through to its end use, Mozzarella cheese undergoes significant transformations in its makeup of components and their structural arrangement. The typical Mozzarella processing steps each alter the structural configuration of the system. The colloidal dispersion of proteins, fat, lactose and minerals that is milk experiences physical, thermal, chemical, biological and ionic induced changes to its composition and structure throughout the manufacturing process and storage. This review critically evaluates the literature related to the structural changes occurring as a result of each step in Mozzarella cheese production process. Emphasis is placed on the role of each step and the induced transformations at the micro and macro scale in the system. Additionally, the review also looks at the changes that occur as a result of storage. This evolution in structure culminates in the creation of an end product with a bi-continuous gel structure that has a desired functionality in its end use.     

Learning and Behavior in Reef Fish: Fuel for Microevolutionary Change?

Small‐scale population differentiation among coral reef fishes may be more common than previously thought. New molecular technologies have informed patterns of differentiation, while experimental approaches focusing on larval abilities to limit distribution have explored processes leading to diversification. Building upon a recently published paper by Wismer et al. that examined population level differences in learning and cooperative behaviors in cleaner wrasse (Labroides dimidiatus), we use a phylogenetic framework to explore how social behaviors are distributed among wrasses in the Labrichthyines clade. Establishing links between social behavior and speciation across the phylogeny allows us explore how social behaviors such as learning and cooperation may also act as possible mechanisms driving diversification at the microevolutionary scale.     

Infrared picosecond laser for perforation of single plant cells

The functional analysis of plant cells at the cellular and subcellular levels requires novel technologies for the directed manipulation of individual cells. In this report, we demonstrate the use of an infrared (1,064 nm) picosecond laser for the perforation of tobacco cell protoplasts. A single pulse was sufficient to perforate the plasma membrane enabling the uptake of dye from the surrounding medium into the cytosol. Moreover, the procedure was shown to be suitable for the efficient delivery of DNA expression constructs to the nucleus, as demonstrated by the subsequent expression and correct targeting of a recombinant fluorescent protein. Single cell perforation using this novel optoporation method shows that isolated plant cells can be permeabilized without direct manipulation. This is a valuable procedure for cell-specific applications, particularly where the import of specific molecules into plant cells is required for functional analysis.     

Steroid transformations by microorgamisms

Microbial transformations of various steroids are reviewed. Newer developments in this field are discussed. A compilation of different steroid substrates used for transformations by various microorganisms during the period 1979–1982, along with the metabolites formed, is included     

Key Innovations: Further Remarks on the Importance of Morphology in Elucidating Systematic Relationships and Adaptive Radiations

The present paper is an argument in support of the continued importance of morphological systematics and a plea for improving molecular phylogenetic analyses by addressing explicit character transformations. We use here the inference of key innovations and adaptive radiations to demonstrate why morphological systematics is still relevant and necessary. After establishing that theories of phylogenetic relationship offer robust explanatory bases for discussing evolutionary diversification, the following topics are addressed: (1) the inference of key innovations grounded in phylogenetic analyses; (2) the epistemic distinction between character ‘mapping’ and relevant evidence in systematic and evolutionary studies; and (3) key innovations in molecular phylogenetics. We emphasize that the discovery of key innovations, in fossil or extant taxa, further strengthens the importance of morphology in systematic and evolutionary inferences, as they reveal scenarios of character transformation that have led to asymmetrical sister-group diversification. Our main conclusion is that understanding characters in and of themselves, when properly contextualized systematically, is what evolutionary biologists should be concerned with, whereas the analysis of tree topology alone, in which statistical nodal support measures are the sole indicators of phylogenetic affinity, does not lead to a fuller understanding of key innovations.     

A diversity-oriented synthesis approach to macrocycles via oxidative ring expansion

Macrocycles are key structural elements in numerous bioactive small molecules and are attractive targets in the diversity-oriented synthesis of natural product-based libraries. However, efficient and systematic access to diverse collections of macrocycles has proven difficult using classical macrocyclization reactions. To address this problem, we have developed a concise, modular approach to the diversity-oriented synthesis of macrolactones and macrolactams involving oxidative cleavage of a bridging double bond in polycyclic enol ethers and enamines. These substrates are assembled in only four or five synthetic steps and undergo ring expansion to afford highly functionalized macrocycles bearing handles for further diversification. In contrast to macrocyclization reactions of corresponding seco acids, the ring expansion reactions are efficient and insensitive to ring size and stereochemistry, overcoming key limitations of conventional approaches to systematic macrocycle synthesis. Cheminformatic analysis indicates that these macrocycles access regions of chemical space that overlap with natural products, distinct from currently targeted synthetic drugs.     

Microbial transformations of tin and tin compounds

Summary The use of organotins for agricultural and industrial purposes and in the marine environment has been increasing steadily for more than 20 years. Recently, reliable methodologies have been developed to permit quantification of individual molecular species of organotins in cultures and in the environment. Particular attention has been given to methyltins which can be formed abiotically and by microorganisms, and to tributyltins which are toxic components of effective antifouling paints. In the aquatic environment tin, tributyltins and other organotins accumulate in the surface microlayer, in sediments, and on suspended particulates. Tin compounds are toxic to a variety of organisms and some aquatic organisms can bioaccumulate them. When tin compounds, particularly di-or tri-substituted tins, enter an ecosystem, a portion of the microbial population is killed. Among the survivors are organisms which can methylate inorganic or organic tins, but the relative contribution of biotic and abiotic mechanisms is not clear. While many details of methylations and demethylations need to be worked out, it is clear that transformations of tins can influence the toxicity, volatility and mobility of tin in natural ecosystems. Tributyltins can be debutylated by microorganisms, and hydroxybutyl tins may be intermediates, as they are in mammalian systems. Little is known of the potential and probable microbial transformations of other economically important organotins, but the transformations should be studied for they may have industrial and environmental importance.     

Steroid transformations by microorganisms—II

Steroid transformations by various microorganisms are reviewed. Newer developments in this area are discussed. A compilation of a variety of steroid substrates used for transformations by microorganisms during the period 1982-mid 1984 along with the metabolites formed, is included.