Insect mitochondrial genomics : implications for evolution and phylogeny

The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.

Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor 1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

Multimedia : a necessary step in the evolution of research funding applications

Multimedia communication capabilities are rapidly expanding, and visual information is easily shared electronically, yet funding bodies still rely on paper grant proposal submissions. Incorporating modern technologies will streamline the granting process by increasing the fidelity of grant communication, improving the efficiency of review, and reducing the cost of the process.

Hydrogen evolution by a metal-free electrocatalyst

Electrocatalytic reduction of water to molecular hydrogen via the hydrogen evolution reaction may provide a sustainable energy supply for the future, but its commercial application is hampered by the use of precious platinum catalysts. All alternatives to platinum thus far are based on nonprecious metals, and, to our knowledge, there is no report about a catalyst for electrocatalytic hydrogen evolution beyond metals. Here we couple graphitic-carbon nitride with nitrogen-doped graphene to produce a metal-free hybrid catalyst, which shows an unexpected hydrogen evolution reaction activity with comparable overpotential and Tafel slope to some of well-developed metallic catalysts. Experimental observations in combination with density functional theory calculations reveal that its unusual electrocatalytic properties originate from an intrinsic chemical and electronic coupling that synergistically promotes the proton adsorption and reduction kinetics.

Using communicative ecology theory to scope the emerging role of social media in the evolution of urban food systems

Urban agriculture plays an increasingly vital role in supplying food to urban populations. Changes in Information and Communications Technology (ICT) are already driving widespread change in diverse food-related industries such as retail, hospitality and marketing. It is reasonable to suspect that the fields of ubiquitous technology, urban informatics and social media equally have a lot to offer the evolution of core urban food systems. We use communicative ecology theory to describe emerging innovations in urban food systems according to their technical, discursive and social components. We conclude that social media in particular accentuate fundamental social interconnections normally effaced by conventional industrialised approaches to food production and consumption.

A model of enterprise architecture evolution

Enterprise architectures are exposed to fast emerging business and information technology capabilities. A prominent example is the paradigm of service-orientation, which leads to its own architectural requirements and impacts the design and ongoing evolution of Enterprise Architectures. This thesis develops the first theoretical model describing enterprise architecture evolution and outcomes in light of a changing IT landscape such as service-oriented architectures. The developed theoretical model explains enterprise architecture evolution, its main stages and related capabilities. This model can be used to derive theoretical, sound guidelines to manage enterprise architectures in a changing environment.

Structural evolution of nanocrystalline silicon thin films synthesized in high-density, low-temperature reactive plasmas

Silicon thin films with a variable content of nanocrystalline phase were deposited on single-crystal silicon and glass substrates by inductively coupled plasma-assisted chemical vapor deposition using a silane precursor without any hydrogen dilution in the low substrate temperature range from 100 to 300 °C. The structural and optical properties of the deposited films are systematically investigated by Raman spectroscopy, x-ray diffraction, Fourier transform infrared absorption spectroscopy, UV/vis spectroscopy, scanning electron microscopy and high-resolution transmission electron microscopy. It is shown that the structure of the silicon thin films evolves from the purely amorphous phase to the nanocrystalline phase when the substrate temperature is increased from 100 to 150 °C. It is found that the variations of the crystalline fraction fc, bonded hydrogen content CH, optical bandgap ETauc, film microstructure and growth rate Rd are closely related to the substrate temperature. In particular, at a substrate temperature of 300 °C, the nanocrystalline Si thin films of our interest feature a high growth rate of 1.63nms-1, a low hydrogen content of 4.0at.%, a high crystalline fraction of 69.1%, a low optical bandgap of 1.55eV and an almost vertically aligned columnar structure with a mean grain size of approximately 10nm. It is also shown that the low-temperature synthesis of nanocrystalline Si thin films without any hydrogen dilution is attributed to the outstanding dissociation ability of the high-density inductively coupled plasmas and effective plasma-surface interactions during the growth process. Our results offer a highly effective yet simple and environmentally friendly technique to synthesize high-quality nanocrystalline Si films, vitally needed for the development of new-generation solar cells and other emerging nanotechnologies.

Evolution of Langmuir waves in a plasma contaminated by variable-charge impurities

The propagation of Langmuir waves in nonisothermal plasmas contaminated by fine dust particles with variable charge is investigated for a self-consistent closed system. Dust charge relaxation, ionization, recombination, and collisional dissipation are taken into account. It is shown that the otherwise unstable coupling of the Langmuir and dust-charge relaxation modes becomes stable and the Langmuir waves are frequency down-shifted.

Molecular phylogeny, biogeography, and habitat preference evolution of marsupials

Marsupials exhibit great diversity in ecology and morphology. However, compared to their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene, and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Evolution to a chronic disease niche correlates with increased sensitivity to tryptophan availability for the obligate intracellular bacterium Chlamydia pneumoniae

The chlamydiae are obligate intracellular parasites that have evolved specific interactions with their various hosts and host cell types to ensure their successful survival and consequential pathogenesis. The species Chlamydia pneumoniae is ubiquitous, with serological studies showing that most humans are infected at some stage in their lifetime. While most human infections are asymptomatic, C. pneumoniae can cause more-severe respiratory disease and pneumonia and has been linked to chronic diseases such as asthma, atherosclerosis, and even Alzheimer's disease. The widely dispersed animal-adapted C. pneumoniae strains cause an equally wide range of diseases in their hosts. It is emerging that the ability of C. pneumoniae to survive inside its target cells, including evasion of the host's immune attack mechanisms, is linked to the acquisition of key metabolites. Tryptophan and arginine are key checkpoint compounds in this host-parasite battle. Interestingly, the animal strains of C. pneumoniae have a slightly larger genome, enabling them to cope better with metabolite restrictions. It therefore appears that as the evolutionarily more ancient animal strains have evolved to infect humans, they have selectively become more "susceptible" to the levels of key metabolites, such as tryptophan. While this might initially appear to be a weakness, it allows these human C. pneumoniae strains to exquisitely sense host immune attack and respond by rapidly reverting to a persistent phase. During persistence, they reduce their metabolic levels, halting progression of their developmental cycle, waiting until the hostile external conditions have passed before they reemerge.

A critical realist perspective of Enterprise Architecture evolution : conditioning and outcomes

This paper investigates how Enterprise Architecture (EA) evolves due to emerging trends. It specifically explores how EA integrates the Service-oriented Architecture (SOA). Archer’s Morphogenetic theory is used as an analytical approach to distinguish the architectural conditions under which SOA is introduced, to study the relationships between these conditions and SOA introduction, and to reflect on EA evolution (elaborations) that then take place. The paper focuses on reasons for why EA evolution could take place, or not and what architectural changes could happen due to SOA integration. The research builds on sound theoretical foundations to discuss EA evolution in a field that often lacks a solid theoretical groundwork. Specifically, it proposes that critical realism, using the morphogenetic theory, can provide a useful theoretical foundation to study enterprise architecture (EA) evolution. The initial results of a literature review (a-priori model) were extended using explorative interviews. The findings of this study are threefold. First, there are five different levels of EA-SOA integration outcomes. Second, a mature EA, flexible and well-defined EA framework and comprehensive objectives of EA improve the integration outcomes. Third, the analytical separation using Archer’s theory is helpful in order to understand how these different integration outcomes are generated.