Bioturbation in matgrounds at Lake Bogoria in the Kenya Rift Valley: implications for interpreting the heterogeneous early Cambrian seafloor

Modern burrowing organisms feed on microbial organic matter in matgrounds near hot springs on the margins of Lake Bogoria, a saline alkaline lake in the Kenya Rift Valley. The burrowers produce a low-diversity trace assemblage similar to those produced by undermat miners during the Ediacaran–Cambrian transition. Despite obvious differences in body plans and phylogenetic affinities, these modern animals feed on microbes in similar ways to those inferred for primitive bilaterians. With increasing distance from hot-spring vents, outflow channels and adjacent matgrounds, the diversity and depth of the traces increase and mixgrounds become dominant. This modern extreme environment gives clues for interpreting the heterogeneous early Cambrian seafloor, with: (1) the restriction of ‘pre-agronomic revolution’ matground substrates; and (2) expansion of adjacent ‘post-agronomic revolution’ mixground areas.     

Complete mitochondrial genomes offer insights into the evolutionary relationships and comparative genetic diversity of New Zealand’s iconic kiwi (Apteryx spp.)

ABSTRACT

Kiwis (Apterygidae) are an enigmatic family of flightless birds endemic to New Zealand. Apterygidae is made up of a single genus, Apteryx with five species, four of which are characterised as at risk of greater by the New Zealand Department of Conservation. These five species are further separated into two morphologically and genetically distinguishable clades, containing A.haastii, and A.owenii in one and A.rowi, A.mantelli, and A.australis in the other. We reconstructed 17 kiwi mitochondrial genomes from previously published genomic data, nine from A.rowi and eight from A.owenii. Mitochondrial diversity analyses uncovered low levels of genetic diversity consistent with their reduced ranges and conservation concern. We further used one of the assembled A.rowi mitochondrial genomes together with mitochondrial genomes from A.haastii, A.owenii, A.mantelli, and several other individuals from Palaeognathae to estimate the within and between clade divergence times of kiwis. Our study exemplifies how available published data can be used in novel ways to provide new and complementary evolutionary insights to previous studies.     

Conformational diversity of the quercetin molecule: a quantum-chemical view

Abstract

This paper focuses on the comprehensive conformational analysis of the quercetin molecule with a broad range of the therapeutic and biological actions. All possible conformers of these molecule, corresponding to the local minima on the potential energy hypersurface, have been obtained by the sequential rotation of its five hydroxyl groups and also by the rotation of its (A?+?C) and B rings relatively each other. Altogether, it was established 48 stable conformers, among which 24 conformers possess planar structure and 24 conformers – nonplanar structure. Their structural, symmetrical, energetical and polar characteristics have been investigated in details. Quantum-mechanical calculations indicate that conformers of the quercetin molecule are polar structures with a dipole moment, which varies within the range from 0.35 to 9.87 Debay for different conformers. Relative Gibbs free energies of these conformers are located within the range from 0.0 to 25.3?kcal·mol^?1 in vacuum under normal conditions. Impact of the continuum with ε?=?4 leads to the decreasing of the Gibbs free energies (–0.19–18.15?kcal·mol^?1) and increasing of the dipole moment (0.57–12.48?D). It was shown that conformers of the quercetin molecule differ from each other by the intramolecular specific contacts (two or three), stabilizing all possible conformers of the molecule – H-bonds (both classical ОН…О and so-called unusual С′Н…О and ОН…С′) and attractive van-der-Waals contacts О…О. Obtained conformational analysis for the quercetin molecule enables to provide deeper understanding of the ‘structure-function’ relationship and also to suggest its mechanisms of the therapeutic and biological actions.

Communicated by Ramaswamy H. Sarma     

Expression of the Arcelin 1 gene from Phaseolus vulgaris L. in cowpea seeds (Vigna unguiculata L.) confers bruchid resistance

Persistent decrease in the productivity of cowpea (Vigna unguiculata L.) has been partly due to attack by bruchids including Zabrotes subfasciatus and Callosobruchus maculatus. Resistance to these insects in Phaseolus vulgaris L. has been shown to be associated with arcelins, a family of seed proteins encoded by a multigenic family of lectins on the APA locus. In this work, we report the construction of an expression vector containing Arc1 gene isolated from P. vulgaris and introduced into cowpea as a strategy to confer resistance to insect attack. Following transformation and selection, feeding experiments in which C. maculatus and Z. subfasciatus were fed with transgenic (L3 and L5) and non-transgenic (control) grains showed that introduced gene protected the transgenic line. Significant differences (p < .05 and p < .01) were found in the number of eggs laid, the number of emerging insects and the loss of grain mass in L3, compared with control, for both insects. Similar observations were made in L5 with the exception of the number of laid eggs. The strategy here described may form the basis for the development of a cowpea variety tolerant to bruchids in a crop cultivated by farmers throughout Latin America and Africa.     

The role of organic amendments to soil for crop protection: Induction of suppression of soilborne pathogens

Application of external organic inputs to soils can be considered as one of the most ancient strategies in agriculture, and it has been commonly used since the very beginning of human-based agricultural practices. During all this time, application of several organic matters to agricultural soils has demonstrated their benefit to plants and soils. Organic amendments have proved to be useful in recovering soil properties, improving soil quality and, in some cases, can be directly involved in providing beneficial effects to plants. All these obtained effects finally lead to an increase in crop protection and sustainability. One most expected effect caused by the application of organic amendments, is the suppression of a wide range of soilborne pathogens (mainly bacterial and fungal pathogens) due to the induction of physicochemical and biological changes in soils. In order to get insight into the nature of the induced soil suppression of soilborne plant pathogens, the analysis of the physical, chemical and the microbial changes, pointed to the key role of beneficial activities produced by soil microorganisms finally adapted to the environmental changes produced by the influence of organic amendments. As shown in the case studies reported here, participation of soil microbes specifically selected after organic amendment is crucial in the control of fungal soilborne diseases. Moreover, the development of “omics” approaches allowed these recent studies to go one step further, revealing the main actors involved in the induced soil suppressiveness and their activities. Thus “omics” techniques will help to understand the soil and its microbiome as a whole system, and to assign the important roles of its biological components.     

Tropical forest loss drives divergent patterns in functional diversity of forest and non-forest birds

Tropical forests have been facing high rates of deforestation driven by multiple anthropogenic disturbances, with severe consequences for biodiversity. However, the understanding of such effects on functional diversity is still limited in tropical regions, especially considering different ecological groups responses. Here, we evaluated the functional responses of birds to forest loss at the threatened Brazilian Atlantic forest, considering the complete assemblage, and both forest-dependent and non-forest-dependent species. Birds were surveyed in 40 forest sites with a forest cover gradient, located in two regions showing different land use types. We tested different models to assess the responses of functional diversity indices to forest loss in these sites. Although functional diversity did not differ between regions, forest and non-forest birds showed divergent responses to forest loss. Deforested landscapes presented an increase in functional richness (SESFRic) and evenness for forest species and an increase of functional dispersion for non-forest birds. Additionally, forested landscapes harbor birds presenting lower body mass and wing length, and non-forest species with lower tarsus length. The maintenance of some functional metrics through forest loss resulted from a compensatory dynamic between forest and non-forest birds, indicating that only evaluating the complete assemblage may mask important idiosyncratic patterns of different ecological groups. Although non-forest species are relatively capable to maintain bird functional diversity in deforested landscapes, forest birds are facing a drastic ongoing collapse in these sites, representing an alarming signal for the maintenance of forest ecosystem function.     

Reprogramming of sugar transport pathways in Escherichia coli using a permeabilized SecY protein-translocation channel

In the initial step of sugar metabolism, sugar-specific transporters play a decisive role in the passage of sugars through plasma membranes into cytoplasm. The SecY complex (SecYEG) in bacteria forms a membrane channel responsible for protein translocation. The present work shows that permeabilized SecY channels can be used as nonspecific sugar transporters in Escherichia coli. SecY with the plug domain deleted allowed the passage of glucose, fructose, mannose, xylose, and arabinose, and, with additional pore-ring mutations, facilitated lactose transport, indicating that sugar passage via permeabilized SecY was independent of sugar stereospecificity. The engineered E. coli showed rapid growth on a wide spectrum of monosaccharides and benefited from the elimination of transport saturation, improvement in sugar tolerance, reduction in competitive inhibition, and prevention of carbon catabolite repression, which are usually encountered with native sugar uptake systems. The SecY channel is widespread in prokaryotes, so other bacteria may also be engineered to utilize this system for sugar uptake. The SecY channel thus provides a unique sugar passageway for future development of robust cell factories for biotechnological applications.