Widespread impact of horizontal gene transfer on plant colonization of land

In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants

CO2 dissolution and design aspects of a multiorifice oscillatory baffled column

Dissolution of CO2 in water was studied for a batch vertical multiorifice baffled column (MOBC) with varying orifice diameters (d0) of 6.4-30 mm and baffle open area (α) of 15-42%. Bubble size distributions (BSDs) and the overall volumetric CO2 mass transfer coefficient (KLa) were experimentally evaluated for very low superficial gas velocities, UG of 0.12-0.81 mm s-1, using 5% v/v CO2 in the inlet gas stream at a range of fluid oscillations (f = 0-10 Hz and x0 = 0-10 mm). Remarkably, baffles presenting large do = 30 mm and α = 36%, therefore in the range typically found for single-orifice oscillatory baffled columns, were outperformed with respect to BSD control and CO2 dissolution by the other baffle designs or the same aerated column operating without baffles or fluid oscillations. Flow visualization and bubble tracking experiments also presented in this study established that a small do of 10.5 mm combined with a small value of α = 15% generates sufficient, strong eddy mixing capable of generating and trapping an extremely large fraction of microbubbles in the MOBC. This resulted in increased interfacial area yielding KLa values up to 65 ± 12 h-1 in the range of the UG tested, representing up to 3-fold increase in the rate of CO2 dissolution when compared to the unbaffled, steady column. In addition, a modi fied oscillatory Reynolds number, Re′o and Strouhal number, St' were presented to assist on the design and scale-up of gas-liquid systems based on multiorifice oscillatory ba ffled columns. This work is relevant to gas-liquid or multiphase chemical and biological systems relying on efficient dissolution of gaseous compounds into a liquid medium.BBSRC -European Commissio

Loss of Genetic Redundancy in Reductive Genome Evolution

Biological systems evolved to be functionally robust in uncertain environments, but also highly adaptable. Such robustness is partly achieved by genetic redundancy, where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of performing, to a limited extent, the same function. Highly variable environments require very robust systems. Conversely, predictable environments should not place a high selective value on robustness. Here we test this hypothesis by investigating the evolutionary dynamics of genetic redundancy in extremely reduced genomes, found mostly in intracellular parasites and endosymbionts. By combining data analysis with simulations of genome evolution we show that in the extensive gene loss suffered by reduced genomes there is a selective drive to keep the diversity of protein families while sacrificing paralogy. We show that this is not a by-product of the known drivers of genome reduction and that there is very limited convergence to a common core of families, indicating that the repertoire of protein families in reduced genomes is the result of historical contingency and niche-specific adaptations. We propose that our observations reflect a loss of genetic redundancy due to a decreased selection for robustness in a predictable environment

Electrostatic phase separation: a review

The current understanding and developments in the electrostatic phase separation are reviewed. The literature covers predominantly two immiscible and inter-dispersed liquids following the last review on the topic some 15 years. Electrocoalescence kinetics and governing parameters, such as the applied field, liquid properties, drop shape and flow, are considered. The unfavorable effects, such as chain formation and partial coalescence, are discussed in detail. Moreover, the prospects of microfluidics platforms, non-uniform fields, coalescence on the dielectric surfaces to enhance the electrocoalescence rate are also considered. In addition to the electrocoalescence in water-in-oil emulsions the research in oil-in-oil coalescence is also discussed. Finally the studies in electrocoalescer development and commercial devices are also surveyed. The analysis of the literature reveals that the use of pulsed DC and AC electric fields is preferred over constant DC fields for efficient coalescence; but the selection of the optimum field frequency a priori is still not possible and requires further research. Some recent studies have helped to clarify important aspects of the process such as partial coalescence and drop–drop non-coalescence. On the other hand, some key phenomena such as thin film breakup and chain formation are still unclear. Some designs of inline electrocoalescers have recently been proposed; however with limited success: the inadequate knowledge of the underlying physics still prevents this technology from leaving the realm of empiricism and fully developing in one based on rigorous scientific methodology

High Confidence Prediction of Essential Genes in Burkholderia Cenocepacia

BACKGROUND: Essential genes are absolutely required for the survival of an organism. The identification of essential genes, besides being one of the most fundamental questions in biology, is also of interest for the emerging science of synthetic biology and for the development of novel antimicrobials. New antimicrobial therapies are desperately needed to treat multidrug-resistant pathogens, such as members of the Burkholderia cepacia complex. METHODOLOGY/PRINCIPAL FINDINGS: We hypothesize that essential genes may be highly conserved within a group of evolutionary closely related organisms. Using a bioinformatics approach we determined that the core genome of the order Burkholderiales consists of 649 genes. All but two of these identified genes were located on chromosome 1 of Burkholderia cenocepacia. Although many of the 649 core genes of Burkholderiales have been shown to be essential in other bacteria, we were also able to identify a number of novel essential genes present mainly, or exclusively, within this order. The essentiality of some of the core genes, including the known essential genes infB, gyrB, ubiB, and valS, as well as the so far uncharacterized genes BCAL1882, BCAL2769, BCAL3142 and BCAL3369 has been confirmed experimentally in B. cenocepacia. CONCLUSIONS/SIGNIFICANCE: We report on the identification of essential genes using a novel bioinformatics strategy and provide bioinformatics and experimental evidence that the large majority of the identified genes are indeed essential. The essential genes identified here may represent valuable targets for the development of novel antimicrobials and their detailed study may shed new light on the functions required to support life

Systematic Mutational Analysis of the Intracellular Regions of Yeast Gap1 Permease

The yeast general amino acid permease Gap1 is a convenient model for studying the intracellular trafficking of membrane proteins. Present at the plasma membrane when the nitrogen source is poor, it undergoes ubiquitin-dependent endocytosis and degradation upon addition of a good nitrogen source, e.g. ammonium. It comprises 12 transmembrane domains (TM) flanked by cytosol-facing N- and C-terminal tails (NT, CT). The NT of Gap1 contains the acceptor lysines for ubiquitylation and its CT includes a sequence essential to exit from the endoplasmic reticulum (ER).Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution

Background: Genome reduction is a common evolutionary process affecting bacterial lineages that establish symbiotic or pathogenic associations with eukaryotic hosts. Such associations yield highly reduced genomes with greatly streamlined metabolic abilities shaped by the type of ecological association with the host. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, represents one of the few complete genomes available of a bacterium at the initial stages of this process. In the present study, genome reduction is studied from a systems biology perspective through the reconstruction and functional analysis of genome-scale metabolic networks of S. glossinidius. Results: The functional profile of ancestral and extant metabolic networks sheds light on the evolutionary events underlying transition to a host-dependent lifestyle. Meanwhile, reductive evolution simulations on the extant metabolic network can predict possible future evolution of S. glossinidius in the context of genome reduction. Finally, knockout simulations in different metabolic systems reveal a gradual decrease in network robustness to different mutational events for bacterial endosymbionts at different stages of the symbiotic association. Conclusions: Stoichiometric analysis reveals few gene inactivation events whose effects on the functionality of S. glossinidius metabolic systems are drastic enough to account for the ecological transition from a free-living to hostdependent lifestyle. The decrease in network robustness across different metabolic systems may be associated with th

The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii

In an effort to understand how a tick-borne pathogen adapts to the body louse, we sequenced and compared the genomes of the recurrent fever agents Borrelia recurrentis and B. duttonii. The 1,242,163–1,574,910-bp fragmented genomes of B. recurrentis and B. duttonii contain a unique 23-kb linear plasmid. This linear plasmid exhibits a large polyT track within the promoter region of an intact variable large protein gene and a telomere resolvase that is unique to Borrelia. The genome content is characterized by several repeat families, including antigenic lipoproteins. B. recurrentis exhibited a 20.4% genome size reduction and appeared to be a strain of B. duttonii, with a decaying genome, possibly due to the accumulation of genomic errors induced by the loss of recA and mutS. Accompanying this were increases in the number of impaired genes and a reduction in coding capacity, including surface-exposed lipoproteins and putative virulence factors. Analysis of the reconstructed ancestral sequence compared to B. duttonii and B. recurrentis was consistent with the accelerated evolution observed in B. recurrentis. Vector specialization of louse-borne pathogens responsible for major epidemics was associated with rapid genome reduction. The correlation between gene loss and increased virulence of B. recurrentis parallels that of Rickettsia prowazekii, with both species being genomic subsets of less-virulent strains