Conservation of geosites as a tool to protect geoheritage: the inventory of Ceará Central Domain, Borborema Province - NE/Brazil

The Ceará Central Domain, in the northern Borborema Province/NE Brazil, encompasses important geological records (geosites) which allow understanding a relevant period of the Earth’s evolution, mainly associated to Neoproterozoic Brazilian/Pan-African Cycle and West Gondwana amalgamation, besides Neoarchean to Ordovician records. The presented geoheritage inventory aims to characterise the geosites with scienti c relevance of Ceará Central Domain. By applying a method for large areas, the nal selection resulted in eight geological frameworks represented by 52 geosites documented in a single database. This is the rst step for a geoconservation strategy based on systematic inventories, statutory protection, geoethical behaviour and awareness about scienti c, educational and/or cultural relevance of geosites.We specially thank all experts that helped us with this inventory: Afonso Almeida, Carlos E.G. de Araújo, César Veríssimo, Christiano Magini, Clóvis Vaz Parente, Felipe G. Costa, Irani C. Mattos, Neivaldo de Castro, Otaciel de Melo, Sebástian G. Chiozza, Ticiano Santos and Stefano Zincone. We are also thankful to Kátia Mansur, Ricardo Fraga Pereira and anonymous reviewers for their valuable contributions. PM is grateful to Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for PhD mobility scholarship PDSE Program/Process n 88881.132168/2016-01info:eu-repo/semantics/publishedVersio

Natural computation meta-heuristics for the in silico optimization of microbial strains

<p>Abstract</p> <p>Background</p> <p>One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only due to the inherent complexity of the metabolic and regulatory networks, but also to the lack of appropriate modelling and optimization tools. To this end, Evolutionary Algorithms (EAs) have been proposed for <it>in silico </it>metabolic engineering, for example, to identify sets of gene deletions towards maximization of a desired physiological objective function. In this approach, each mutant strain is evaluated by resorting to the simulation of its phenotype using the Flux-Balance Analysis (FBA) approach, together with the premise that microorganisms have maximized their growth along natural evolution.</p> <p>Results</p> <p>This work reports on improved EAs, as well as novel Simulated Annealing (SA) algorithms to address the task of <it>in silico </it>metabolic engineering. Both approaches use a variable size set-based representation, thereby allowing the automatic finding of the best number of gene deletions necessary for achieving a given productivity goal. The work presents extensive computational experiments, involving four case studies that consider the production of succinic and lactic acid as the targets, by using <it>S. cerevisiae </it>and <it>E. coli </it>as model organisms. The proposed algorithms are able to reach optimal/near-optimal solutions regarding the production of the desired compounds and presenting low variability among the several runs.</p> <p>Conclusion</p> <p>The results show that the proposed SA and EA both perform well in the optimization task. A comparison between them is favourable to the SA in terms of consistency in obtaining optimal solutions and faster convergence. In both cases, the use of variable size representations allows the automatic discovery of the approximate number of gene deletions, without compromising the optimality of the solutions.</p

Stochastic Gravity: Theory and Applications

Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein-Langevin equation, which has in addition sources due to the noise kernel. In the first part, we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. In the second part, we describe three applications of stochastic gravity theory. First, we consider metric perturbations in a Minkowski spacetime, compute the two-point correlation functions of these perturbations and prove that Minkowski spacetime is a stable solution of semiclassical gravity. Second, we discuss structure formation from the stochastic gravity viewpoint. Third, we discuss the backreaction of Hawking radiation in the gravitational background of a black hole and describe the metric fluctuations near the event horizon of an evaporating black holeComment: 100 pages, no figures; an update of the 2003 review in Living Reviews in Relativity gr-qc/0307032 ; it includes new sections on the Validity of Semiclassical Gravity, the Stability of Minkowski Spacetime, and the Metric Fluctuations of an Evaporating Black Hol

Chemodynamics of the Milky Way. I. The first year of APOGEE data

We investigate the chemo-kinematic properties of the Milky Way disc by exploring the first year of data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE), and compare our results to smaller optical high-resolution samples in the literature, as well as results from lower resolution surveys such as GCS, SEGUE and RAVE. We start by selecting a high-quality sample in terms of chemistry (____sim 20.000 stars) and, after computing distances and orbital parameters for this sample, we employ a number of useful subsets to formulate constraints on Galactic chemical and chemodynamical evolution processes in the Solar neighbourhood and beyond (e.g., metallicity distributions -- MDFs, [____alpha/Fe] vs. [Fe/H] diagrams, and abundance gradients). Our red giant sample spans distances as large as 10 kpc from the Sun. We find remarkable agreement between the recently published local (d $<$ 100 pc) high-resolution high-S/N HARPS sample and our local HQ sample (d $<$ 1 kpc). The local MDF peaks slightly below solar metallicity, and exhibits an extended tail towards [Fe/H] $= -$1, whereas a sharper cut-off is seen at larger metallicities. The APOGEE data also confirm the existence of a gap in the [____alpha/Fe] vs. [Fe/H] abundance diagram. When expanding our sample to cover three different Galactocentric distance bins, we find the high-[____alpha/Fe] stars to be rare towards the outer zones, as previously suggested in the literature. For the gradients in [Fe/H] and [____alpha/Fe], measured over a range of 6 $<$ R $<$ 11 kpc in Galactocentric distance, we find a good agreement with the gradients traced by the GCS and RAVE dwarf samples. For stars with 1.5 $<$ z $<$ 3 kpc, we find a positive metallicity gradient and a negative gradient in [____alpha/Fe]

High-Efficiency Stem Cell Fusion-Mediated Assay Reveals Sall4 as an Enhancer of Reprogramming

Several methods allow reprogramming of differentiated somatic cells to embryonic stem cell-like cells. However, the process of reprogramming remains inefficient and the underlying molecular mechanisms are poorly understood. Here, we report the optimization of somatic cell fusion with embryonic stem cells in order to provide an efficient, quantitative assay to screen for factors that facilitate reprogramming. Following optimization, we achieved a reprogramming efficiency 15–590 fold higher than previous protocols. This allowed observation of cellular events during the reprogramming process. Moreover, we demonstrate that overexpression of the Spalt transcription factor, Sall4, which was previously identified as a regulator of embryonic stem cell pluripotency and early mouse development, can enhance reprogramming. The reprogramming activity of Sall4 is independent of an N-terminal domain implicated in recruiting the nucleosome remodeling and deacetylase corepressor complex, a global transcriptional repressor. These results indicate that improvements in reprogramming assays, including fusion assays, may allow the systematic identification and molecular characterization of enhancers of somatic cell reprogramming