On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype

If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although 'Loki' cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon

Tuning Genetic Clocks Employing DNA Binding Sites

Periodic oscillations play a key role in cell physiology from the cell cycle to circadian clocks. The interplay of positive and negative feedback loops among genes and proteins is ubiquitous in these networks. Often, delays in a negative feedback loop and/or degradation rates are a crucial mechanism to obtain sustained oscillations. How does nature control delays and kinetic rates in feedback networks? Known mechanisms include proper selection of the number of steps composing a feedback loop and alteration of protease activity, respectively. Here, we show that a remarkably simple means to control both delays and effective kinetic rates is the employment of DNA binding sites. We illustrate this design principle on a widely studied activator-repressor clock motif, which is ubiquitous in natural systems. By suitably employing DNA target sites for the activator and/or the repressor, one can switch the clock “on” and “off” and precisely tune its period to a desired value. Our study reveals a design principle to engineer dynamic behavior in biomolecular networks, which may be largely exploited by natural systems and employed for the rational design of synthetic circuits.United States. Air Force Office of Scientific Research (Grant FA9550-09-1-0211)National Science Foundation (U.S.). (Communication and Information Foundations) (Grant 1058127

On the Sensitivity of the West Caribbean Sea Circulation to Tides, Wind, and Mesoscale Ocean Eddies: A Three-Dimensional Ocean Model Study

A three-dimensional, primitive equation ocean model is used to study the circulation in the West Caribbean Sea (WCS) region, and to test the sensitivity of the coastal flow to various forcing fields such as tides, climatological wind, and Caribbean eddies. The model domain is bordered by latitudes 15 – 22 degrees N and longitudes 76 – 87 degrees W, with the MesoAmerican Barrier Reef System (MBRS, along the coasts of Mexico, Belize, Guatemala, and Honduras) and the southern coast of Cuba as land boundaries. The WCS is open to the Caribbean Sea in the southeast and the Yucatan Channel in the northwest, with a prescribed 25 Sv flow-through from southeast to northwest. The results show that the base flow is highly variable even without time dependent forcing and without assimilation of eddies. The interaction of the base flow with the bathymetry gives rise to frequent westward propagating cyclonic eddies with diameters of 50-150 km in the Gulf of Honduras, and an anticyclonic eddy southeast of the Yucatan Channel with diameter of 200 km. When mesoscale eddies are included in the initial condition through assimilation of altimeter data, the WCS model simulates the propagation of those eddies, so that the eddy field is quite realistic even after 45 days from the initialization. Moreover, eddies were found to influence the coastal flow, such that when a cyclonic or an anticyclonic eddy is propagating through the WCS, the velocity field along the MBRS is either attenuated or enhanced, respectively. The area-averaged mean surface kinetic energy is influenced mostly by the 25 Sv flow-through and climatological winds, while the area- averaged eddy surface kinetic energy is influenced mostly by the mesoscale Caribbean eddies

Simulations of the Influence of the West Caribbean Sea Circulation and Eddies on the Meso-American Barrier Reef System

The Meso-American Barrier Reef System (MBRS) along the coasts of Mexico, Belize, Guatemala, and Honduras is an ecologically and biologically sensitive region. It provides for example, major spawning aggregation sites for various species of fish; these activities may be influenced by variations of the flow near the reef and the transports between the MBRS and the Caribbean Sea circulation. Caribbean eddies, which may play an important role in flow variability, have been studied in the past by observations and models (Carton and Chao, 1999; Murphy et al., 1999; Andrade and Barton, 2000; Oey et al., 2003), but knowledge of their influence on the MBRS is still not complete. With limited availability of long-term observations near the reef and coast, as well as in the open Caribbean Sea, hydrodynamic numerical ocean models may provide important means to study this region

The tree of life : the powerful mathematical idea at the heart of evolution

The way in which all living things — from microscopic bacteria to human beings to giant sequoia — are related to one another follows a deep and unexpected mathematical pattern, which we now know as the 'tree of life'. This pattern was discovered by naturalists over centuries, but it was Charles Darwin and Alfred Russel Wallace who realised that it held the key to understanding the origin and diversity of life on Eart

Modeling of the Bacterial Mechanism of Methicillin-Resistance by a Systems Biology Approach

BACKGROUND: A microorganism is a complex biological system able to preserve its functional features against external perturbations and the ability of the living systems to oppose to these external perturbations is defined "robustness". The antibiotic resistance, developed by different bacteria strains, is a clear example of robustness and of ability of the bacterial system to acquire a particular functional behaviour in response to environmental changes. In this work we have modeled the whole mechanism essential to the methicillin-resistance through a systems biology approach. The methicillin is a beta-lactamic antibiotic that act by inhibiting the penicillin-binding proteins (PBPs). These PBPs are involved in the synthesis of peptidoglycans, essential mesh-like polymers that surround cellular enzymes and are crucial for the bacterium survival. METHODOLOGY: The network of genes, mRNA, proteins and metabolites was created using CellDesigner program and the data of molecular interactions are stored in Systems Biology Markup Language (SBML). To simulate the dynamic behaviour of this biochemical network, the kinetic equations were associated with each reaction. CONCLUSIONS: Our model simulates the mechanism of the inactivation of the PBP by methicillin, as well as the expression of PBP2a isoform, the regulation of the SCCmec elements (SCC: staphylococcal cassette chromosome) and the synthesis of peptidoglycan by PBP2a. The obtained results by our integrated approach show that the model describes correctly the whole phenomenon of the methicillin resistance and is able to respond to the external perturbations in the same way of the real cell. Therefore, this model can be useful to develop new therapeutic approaches for the methicillin control and to understand the general mechanism regarding the cellular resistance to some antibiotics