Involvement of the Global Crp Regulator in Cyclic AMP-Dependent Utilization of Aromatic Amino Acids by Pseudomonas putida

The phhAB operon encodes a phenylalanine hydroxylase involved in the conversion of l-phenylalanine into l-tyrosine in Pseudomonas putida. The phhAB promoter is transcribed by RNA polymerase sigma-70 and is unusual in that the specific regulator PhhR acts as an enhancer protein that binds to two distant upstream sites (−75 to −92 and −132 to −149). There is an integration host factor (IHF) binding site that overlaps the proximal PhhR box, and, consequently, IHF acts as an inhibitor of transcription. Use of l-phenylalanine is compromised in a crp-deficient background due to reduced expression from the phhAB promoter. Electrophoretic mobility shift assays and DNase I footprinting assays reveal that Crp binds at a site centered at −109 only in the presence of cyclic AMP (cAMP). We show, using circular permutation analysis, that the simultaneous binding of Crp/cAMP and PhhR bends DNA to bring positive regulators and RNA polymerase into close proximity. This nucleoprotein complex promotes transcription from phhA only in response to l-phenylalanine

A unified model framework for the multiattribute consistent periodic vehicle routing problem

Modeling real-life transportation problems usually require the simultaneous incorporation of different variants of the classical vehicle routing problem (VRP). The periodic VRP (PVRP) is a classical extension in which routes are determined for a planning period of several days and each customer has an associated set of allowable visit schedules. This work proposes a unified model framework for PVRP that consists of multiple attributes or variants not previously addressed simultaneously, such as time-windows, time-dependence, and consistency-which guarantees the visits to customer by the same vehicle-, together with three objective functions that respond to the needs of practical problems. The numerical experimentation is focused on the effects of three factors: frequency, depot centrality, and the objective function on the performance of a general-purpose MILP solver, through the analysis of the achieved relative gaps. Results show higher sensitivity to the objective functions and to the problem sizes. © 2020 Baldoquin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Compromised root development constrains the establishment potential of native plants in unamended alkaline post-mining substrates

© 2018, Springer Nature Switzerland AG. Background and aims: Mined materials often require rehabilitation or ecological restoration through revegetation as part of mine closure and relinquishment practices, yet there is a widening gap between the expectations of recovery and what industry achieve. The edaphic conditions of post-mining substrates present a suite of potential limitations to plant growth and may constrain the establishment capability and development of native species. Methods: We assessed seedling emergence, relative growth rate and calculated standardised growth estimates using 10 measured root and shoot parameters for six locally-dominant native species from different families and nutrient-acquisition strategies in a range of representative mining restoration substrates (topsoil, tailings, capped tailings and waste rock), examining their suitability as pioneers for ecological restoration. Results: The establishment and growth of all six species in post-mining substrates were significantly compromised. Root development was significantly responsive to substrate, with measured root parameters on average 27% lower in capped tailings, 41% lower in waste rock and 67% lower for individuals grown in tailings compared with those grown in topsoil alone. Plant growth was compromised at different life cycle stages (seed germination, seedling establishment, early growth and development) and across a number of different traits, with primary edaphic constraints including high pH (>8.5) and insufficient available N. The highest-performing species on post-mining substrates was an N2-fixing legume, while lowest-performing species included those with ectomycorrhizal associations or no specific nutrient-acquisition strategy. Conclusions: Edaphic filters may be significant drivers of trajectory and success in rehabilitation and restoration projects at scales ranging from individuals (by limiting establishment or constraining growth and development) to communities (by causing species to assemble in a different manner than the desired reference community). If intractable edaphic parameters constraining plant establishment and early development such as extreme pH and a lack of available nutrients are not ameliorated, the restoration trajectory on post-mining landforms is likely unfavourable. Failure to adequately ameliorate post-mining substrates may represent a major liability for industry in meeting mine-closure requirements