Whole Genome Duplications and a ‘Function’ for Junk DNA? Facts and Hypotheses

International audienceBACKGROUND: The lack of correlation between genome size and organismal complexity is understood in terms of the massive presence of repetitive and non-coding DNA. This non-coding subgenome has long been called "junk" DNA. However, it might have important functions. Generation of junk DNA depends on proliferation of selfish DNA elements and on local or global DNA duplication followed by genic non-functionalization. METHODOLOGY/PRINCIPAL FINDINGS: Evidence from genomic analyses and experimental data indicates that Whole Genome Duplications (WGD) are often followed by a return to the diploid state, through DNA deletions and intra/interchromosomal rearrangements. We use simple theoretical models and simulations to explore how a WGD accompanied by sequence deletions might affect the dosage balance often required among several gene products involved in regulatory processes. We find that potential genomic deletions leading to changes in nuclear and cell volume might potentially perturb gene dosage balance. CONCLUSIONS/SIGNIFICANCE: The potentially negative impact of DNA deletions can be buffered if deleted genic DNA is, at least temporarily, replaced by repetitive DNA so that the nuclear/cell volume remains compatible with normal living. Thus, we speculate that retention of non-functionalized non-coding DNA, and replacement of deleted DNA through proliferation of selfish elements, might help avoid dosage imbalances in cycles of polyploidization and diploidization, which are particularly frequent in plants

Problemas cuantitativos y comprensión de conceptos

Los docentes de química a nivel universitario usamos «problemas», habitualmente de tipo cuantitativo, para enseñar y para evaluar. En este trabajo ponemos en duda de que lo hagamos en forma eficaz. Se muestra, a partir de pruebas diagnósticas de pares de problemas (uno cuantitativo y otro cualitativo similar), que muchos estudiantes pueden resolver los problemas cuantitativos sin una adecuada comprensión conceptual.Chemistry professors at university level make use of «problems», usually of a quantitative type, to teach and evaluate. In this article we question the fact of whether they do it in an efficient way. From diagnostic test of pairs of problems (a quantitative and a similar qualitative one) it is shown that many students can solve quantitative problems without an appropriate conceptual comprehension

Statistical Process Control of assembly lines in a manufacturing plant: Process Capability assessment

Among the main strategies adopted by companies for enhancing their competitive advantage as well as for improving the internal efficiency is the quality management. Several tools can be involved when dealing with this issue; one of these is the Statistical Process Control, which includes the employment of statistical methods and metrics to monitor and control a process' quality. In this paper, indeed, two statistical metrics are involved for assessing the process capability of a filler machine produced by an Italian company operating in the food context. Specifically, two processes are inspected: the slewing ring-pinion backlash and the handling clamps height check, both showing excellent performances after having carried out the control and provided appropriate adjustments. Results are also compared with those obtained from the Six Sigma theory, another tool involved for quality controls which is in line with principles of lean manufacturing. Moreover, for the second process, a software was implemented for speeding up operations and achieving benefits in terms of time. The reliability of these analysis is confirmed by the application of the ANOVA Gage R&R tool, which allowed to assess the precision of the measurement system involved

Bulk Cr tips for scanning tunneling microscopy and spin-polarized scanning tunneling microscopy

A simple, reliable method for preparation of bulk Cr tips for Scanning Tunneling Microscopy (STM) is proposed and its potentialities in performing high-quality and high-resolution STM and Spin Polarized-STM (SP-STM) are investigated. Cr tips show atomic resolution on ordered surfaces. Contrary to what happens with conventional W tips, rest atoms of the Si(111)-7x7 reconstruction can be routinely observed, probably due to a different electronic structure of the tip apex. SP-STM measurements of the Cr(001) surface showing magnetic contrast are reported. Our results reveal that the peculiar properties of these tips can be suited in a number of STM experimental situations

Low-frequency modes in the Raman spectrum of sp-sp2 nanostructured carbon

A novel form of amorphous carbon with sp-sp2 hybridization has been recently produced by supersonic cluster beam deposition showing the presence in the film of both polyynic and cumulenic species [L. Ravagnan et al. Phys. Rev. Lett. 98, 216103 (2007)]. Here we present a in situ Raman characterization of the low frequency vibrational region (400-800 cm-1) of sp-sp2 films at different temperatures. We report the presence of two peaks at 450 cm-1 and 720 cm-1. The lower frequency peak shows an evolution with the variation of the sp content and it can be attributed, with the support of density functional theory (DFT) simulations, to bending modes of sp linear structures. The peak at 720 cm-1 does not vary with the sp content and it can be attributed to a feature in the vibrational density of states activated by the disorder of the sp2 phase.Comment: 15 pages, 5 figures, 1 tabl

Pulsed Laser Deposition of two-dimensional ZnO nanocrystals on Au(111): Growth, surface structure and electronic properties

Two-dimensional (2D) ZnO structures have been deposited on the Au(111) surface by means of the pulsed laser deposition (PLD) technique. In situ scanning tunneling microscopy (STM) and spectroscopy (STS) measurements have been performed to characterize morphological, structural and electronic properties of 2D ZnO at the nanoscale. Starting from a sub-monolayer coverage, we investigated the growth of ZnO, identifying different atomic layers (up to the 5th). At low coverage, we observed single- and bi-layer nanocrystals, characterized by a surface moire pattern that is associated to a graphene-like ZnO structure. By increasing the coverage, we revealed a morphological change starting from the 4th layer, which was attributed to a transition toward a bulk-like structure. Investigation of the electronic properties revealed the semiconducting character of 2D ZnO. We observed a dependence of the density of states (DOS) and, in particular, of the conduction band (CB) on the ZnO thickness, with a decreasing of the CB onset energy for increasing thickness. The CB DOS of 2D ZnO shows a step-like behaviour which may be interpreted as due to a 2D quantum confinement effect in ZnO atomic layer

Economic evaluation of automated guided vehicles usage in a food company

Nowadays, companies are more and more attracted and interested by the possibility of automating processes which can be easily carried out by devices or machines instead of employees, allowing saving in costs, higher productivity and flexibility. Among the most spread ways of automating processes, more precisely in this specific case the flow of materials, the Automated Guided Vehicles (AGVs) stand out. But the main question that everyone asks is the following: is it convenient or not? In this paper, the answer is provided for a company operating in the food context, which intends to automate the transport of raw ingredients from the kitchens where they are produced and prepared to the filling lines; to this end, an economic feasibility study is carried out, taking into account three different levels of automation for three different lines. Results from all the three scenarios demonstrate the convenience in terms of achievable revenues, saved hours and manpower, and will support the management in their operational decisions

In vitro antioxidant properties of digests of hydrolyzed casein and caseinophosphopeptide preparations in cell models of human intestine and osteoblasts

Three commercial samples consisting of enriched calcium-free caseinophosphopeptides (CPP), enriched calcium-bound caseinophosphopeptides (Ca-CPP) and an enzymatically hydrolyzed casein (hCN) were in vitro digested according to COST-Infogest protocol. As assessed by UPLC-HR-MS/MS, the digests contained 207\u2013235 unique caseinophosphopeptides, and the species presenting the cluster sssEE were more abundant in CPP digest. The antioxidant activity at three different doses of each digest was firstly evaluated on human intestinal Caco-2/HT-29 70/30 co-culture. In presence of AAPH, hCN and CPP digests displayed a dose-dependent antioxidant activity equal or even greater than Vitamin C. In presence of Fe2+, the digests exerted an antioxidant activity mainly at the highest dose. Antioxidant activities of the intestinal metabolized digests was then evaluated on human osteoblast (Saos-2) cells. The digests exerted an antioxidant activity in presence of AAPH, but not in presence of Fe2+. These results highlight milk-derived peptides as potential dietary supplements for gut and bone health

Pulse-coupled relaxation oscillators: from biological synchronization to Self-Organized Criticality

It is shown that globally-coupled oscillators with pulse interaction can synchronize under broader conditions than widely believed from a theorem of Mirollo \& Strogatz \cite{MirolloII}. This behavior is stable against frozen disorder. Beside the relevance to biology, it is argued that synchronization in relaxation oscillator models is related to Self-Organized Criticality in Stick-Slip-like models.Comment: 4 pages, RevTeX, 1 uuencoded postscript figure in separate file, accepted for publication in Phys. Rev. Lett

Stability of Spatio-Temporal Structures in a Lattice Model of Pulse-Coupled Oscillators

We analyze the collective behavior of a lattice model of pulse-coupled oscillators. By studying the intrinsic dynamics of each member of the population and their mutual interactions we observe the emergence of either spatio-temporal structures or synchronized regimes. We perform a linear stability analysis of these structures.Comment: 15 pages, 2 PostScript available upon request at [email protected], Accepted in Physica