An extension of the coevolution theory of the origin of the genetic code

<p>Abstract</p> <p>Background</p> <p>The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors.</p> <p>Results</p> <p>It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin.</p> <p>Conclusion</p> <p>All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses.</p> <p>Reviewers</p> <p>This article was reviewed by Rob Knight, Paul Higgs (nominated by Laura Landweber), and Eugene Koonin.</p

Environmental Audit improvements in industrial systems through FRAM

Environmental risk management requires specific methodologies to focus audit activities on the most critical elements of production systems. Limited resources require a clear motivation to put attention on specific technological, human, organizational components, and often should address the monitor of interactions among these elements. Recent research in environmental risk looks at methods to deal with complexity as interesting tools to reduce real impacts on pollution and consumption. In this paper, we provide evidence of the advantage in using the Functional Resonance Analysis Method (FRAM), not only to identify the criticalities of a complex production system but to provide a methodology to continuously improve the audit activities in parallel with the introduction of technique to reduce environmental risk. The case study presents the evolution of environmental audit in a sinter plant, proving the need for a review of the criticality list and the successful application of FRAM to refocus the control activities

The Origin of the Genetic Code: Matter of Metabolism or Physicochemical Determinism?

n/

Simulation model of the logistic distribution in a medical oxygen supply chain

Research activities on operations management in the last years are always more dedicated to supply chain and logistics optimization models. The study belongs to this branch and describes the problems related to a re-configuration of the distribution net in a company that produces medical oxygen cylinders for Italian market. The enterprise is particularly sensible to the optimization of supplying processes due to the characteristics of its product, as any delay in the delivery could create dangerous health situation for patients. The work has the objective to realize a software for supply chain management that could be a decision support system, analyzing strategic impacts that changes in distribution system create. In details, the model shows the differences in service level in case of closing one or more factories and the relative necessary changes in logistics net. The paper is articulated in the following parts: • analysis of company and construction of simulation model; • study of classic operation research techniques to solve dynamic vehicle routing problems; • description of possible scenes derived by strategic decision in closing factories; analysis of experiments and global conclusions and developments

Managing the bullwhip effect in multi-echelon supply chains

This editorial article presents the bullwhip effect which is one of the major problems faced by supply chain management. The bullwhip effect represents the demand variability amplification as demand information travels upstream in the supply chain. The bullwhip effect research has been attempting to prove its existence, identify its causes, quantify its magnitude and propose mitigation and avoidance solutions. Previous research has relied on different modeling approaches to quantify the bullwhip effect and to investigate the proposed mitigation/avoidance solutions. Extensive research has shown that smoothing replenishment rules and collaboration in supply chain are the most powerful approaches to counteract the bullwhip effect. The objective of this article is to highlight the bullwhip effect avoidance approaches with providing some interesting directions for future research

Special Issue on the Early Evolution of Life

n/

Enterprise Risk Management to Drive Operations Performances

Global competition characterizes the market of the new millennium where uncertainty and volatility are the main elements affecting the decision making process of managers that need to determine scenarios, define strategies, plan interventions and investments, develop projects and execute operations. Risks have been always part of entrepreneurships but a growing attention to the issues related to Risk Management is nowadays spreading. Along with the financial scandals in the affairs of some major corporations, the high degree of dynamism and the evolutions of markets need organizations to rapidly adapt their business models to changes, whether economic, political, regulatory, technological or social. In particular, managerial trends of business disintegration,decentralization and outsourcing, pushed organizations towards practices of information sharing, coordination and partnership. The difficulties that generally arise during the implementation of these practices underline the impact that critical risk factors can have on corporate governance. Operations, at any level, are highly affected in their performance by uncertainty, reducing their efficiency and effectiveness while losing control on the evolution of the value chain. Studies on risk management have to be extended, involving not only internal processes of companies but considering also the relationship and the level of integration of supply chain partners. This can be viewed as a strategic issue of operations management to enable interventions of research, development and innovation. In a vulnerable economy, where the attention to quality and efficiency through cost reduction is a source of frequent perturbations, an eventual error in understanding the sensibility of the operations to continuous changes can seriously and irreparably compromise the capability of fitting customers’ requirements. While studies and standards on risk management for health and safety, environment or security of information defined a well-known and universally recognized state of the art, corporate and operational risk management already needs a systematic approach and a common view. The main contributions in these fields are the reference models issued by international bodies. Starting from the most advanced international experiences, in this chapter some principles are defined and developed in a framework that, depending on the maturity level of organizations, may help to adequately support their achievements and drive operations performance

Effect of high planting density and foliar fungicide application on the grain maize and silage and methane yield

The research investigated ways to enhance maize yield in intensive maize cropping system by evaluating the effect of high planting densities combined with foliar fungicide treatments. The considered assessments were fungal leaf disease, biomass and grain yield and methane production through anaerobic fermentation. The experiment was conducted in the years 2012 and 2013. The treatments compared at each location were factorial combinations of two plant densities and three fungicide applications. A standard planting density (StD, 7.5 plants m‑2on a 0.75 m inter-row spacing), was compared with the high density (HiD, 10 plants m‑2 onnarrow 0.5 m inter-row spacing). Two fungicides, pyraclostrobin at 0.2 kg AI ha‑1and a mixture of pyraclostrobin and epoxiconazole at 0.2 and 0.075 kg AI ha­‑1respectively, were applied at the tassel emergence stage and compared with an untreated treatment. The HiD system positively increased the silage maize yield (+16%), grain (+17%) and methane yield per hectare (+19%) in comparison to the StD. The fungicide application significantly restrained foliar disease symptoms only in 2012. Fungicide did not affect plant silage composition (protein, starch or fiber content) and methane yield, conversely it significantly increased grain yield for both planting density systems (+5%). The overall boost in yield obtained by combining both strategies in an intensive system, HiD combined with the fungicide, was +24% for methane and +21% for grain yield compared to StD without fungicide application. This work proved that an intensive high planting system with up to 10 plants m‑2, supported by leaf fungicide treatments,can lead to a real yield enhancement of both maize grain and silage

Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains of Pyrococcus abyssi

Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code