Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics ...data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.
The yeast Kluyveromyces marxianus offers unique potential for industrial biotechnology because of useful features like rapid growth, thermotolerance and a wide substrate range. As an emerging ...alternative platform, K. marxianus requires the development and validation of metabolic engineering strategies to best utilise its metabolism as a basis for bio-based production.
To illustrate the synthetic biology strategies to be followed and showcase its potential, we describe a comprehensive approach to rationally engineer a metabolic pathway in K. marxianus. We use the phenylalanine biosynthetic pathway both as a prototype and because phenylalanine is a precursor for commercially valuable secondary metabolites. First, we modify and overexpress the pathway to be resistant to feedback inhibition so as to overproduce phenylalanine de novo from synthetic minimal medium. Second, we assess native and heterologous means to increase precursor supply to the biosynthetic pathway. Finally, we eliminate branch points and competing reactions in the pathway and rebalance precursors to redirect metabolic flux to a specific product, 2-phenylethanol (2-PE). As a result, we are able to construct robust strains capable of producing over 800 mg L
2-PE from minimal medium.
The strains we constructed are a promising platform for the production of aromatic amino acid-based biochemicals, and our results illustrate challenges with attempting to combine individually beneficial modifications in an integrated platform.
In soil, some specific bacterial populations, called plant growth-promoting rhizobacteria are able to promote plant growth and/or reduce the incidence of soil-borne diseases. Rhizosphere competence ...is an important prerequisite for the efficacy of these biocontrol strains. Therefore, over decades, multiple approaches have been combined to understand the molecular basis of bacterial traits involved in rhizosphere competence. This review addresses the bacterial genes expressed during bacterial–plant interactions in the rhizosphere of different plant species. The distribution of these key genes in natural populations of rhizobacteria is also discussed.
In this study involving wives of active-duty U.S. Army soldiers, women whose husbands were deployed to Iraq or Afghanistan between 2003 and 2006 were more likely to receive diagnoses of depressive, ...sleep, anxiety, and stress disorders than were women whose husbands were not deployed.
In this study involving wives of active-duty U.S. Army soldiers, women whose husbands were deployed to Iraq or Afghanistan between 2003 and 2006 were more likely to receive diagnoses of depressive, sleep, anxiety, and stress disorders than were women whose husbands were not deployed.
Mental health research involving past warfare indicates that frequent or extended military deployment leads to increased stress, anxiety, and depression among personnel
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However, current warfare in Iraq and Afghanistan differs greatly from that of other conflicts involving the United States. Combat during the 1991 Gulf War ended quickly and with relatively few U.S. casualties. In contrast, current operations have involved the first sustained ground combat since the Vietnam War, followed by a period of insurgent attacks that regularly maim and kill service personnel. In the same number of months, nearly six times as many hostile . . .
•Falling head (PT) vs constant head (Kfs) hydraulic conductivities across Irish soils.•Reynolds (2008) solution should be used to determine Kfs in Irish context.•PT vs Kfs relationship for Irish ...soils matches more generic formulations closely.•Comparison of international standards for soil treatment units provided.•Irish threshold PT limits for on-site wastewater treatment converted to Kfs values.
The suitability of a location for an on-site wastewater treatment process (for areas which lack access to centralised wastewater treatment systems) requires an assessment of the permeability of the soil into which the effluent will be discharged. In many jurisdictions this is determined using some type of in-situ percolation test. Falling head percolation tests, which give a value of percolation time (PT) that is empirically related to the notion of hydraulic conductivity, are widely used as they are relatively simple to carry out, but the test does not have a sound theoretical framework and test methods are not standardised internationally. In comparison, the saturated hydraulic conductivity of a soil obtained from a constant head well permeameter test is independent of test conditions, and so is a more suitable metric for design. A database of over 900 falling head tests carried out across a range of different subsoil types in Ireland has been collated, all with the inherent limitations of the existing regulative framework regarding the percolation test and soil texture assessment. These tests were then modelled using Hydrus 2-D numerical modelling simulations to determine equivalent field saturated hydraulic conductivity (Kfs) values and thereby provide a correlation with PT values across the range of subsoil conditions. In addition, falling head tests have been carried out in parallel to constant head permeameter tests in the field and compared against the relationship derived from the broad dataset of simulated results. This revealed an optimal solution by which to determine Kfs from the field permeameter test (using parameters recommended for most structured soils from clays to loams). The trendline based on Irish data was also compared against more generic formulations of the relationship between PT, and Kfs and shown to match closely, particularly the Reynolds (2016) ‘unified’ methodology. Finally, the Irish threshold PT limits for on-site wastewater treatment have been converted to Kfs values and compared against other international standards.
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Bacteria encode multiple protein secretion systems that are crucial for interaction with the environment and with hosts. In recent years, attention has focused on type VI secretion systems (T6SSs), ...which are specialized transporters widely encoded in Proteobacteria. The myriad of processes associated with these secretion systems could be explained by subclasses of T6SS, each involved in specialized functions. To assess diversity and predict function associated with different T6SSs, comparative genomic analysis of 34 Pseudomonas genomes was performed. This identified 70 T6SSs, with at least one locus in every strain, except for Pseudomonas stutzeri A1501. By comparing 11 core genes of the T6SS, it was possible to identify five main Pseudomonas phylogenetic clusters, with strains typically carrying T6SSs from more than one clade. In addition, most strains encode additional vgrG and hcp genes, which encode extracellular structural components of the secretion apparatus. Using a combination of phylogenetic and meta-analysis of transcriptome datasets it was possible to associate specific subsets of VgrG and Hcp proteins with each Pseudomonas T6SS clade. Moreover, a closer examination of the genomic context of vgrG genes in multiple strains highlights a number of additional genes associated with these regions. It is proposed that these genes may play a role in secretion or alternatively could be new T6S effectors.
Several different approaches have been developed to model the specific characteristics of karst aquifers, taking account of their inherent complex spatial and temporal heterogeneities. This paper ...sets out the development of a semidistributed modelling approach for applications in an Irish karst context using urban drainage software. The models have proven to be very useful for different studies, with examples given for the ecohydrology of ephemeral karst lakes, extreme groundwater-flood alleviation, karst network investigation, submarine groundwater discharge, and quantification of different recharge and flow components. The limitations of the approach are also highlighted, in particular not being able to simulate diffuse infiltration and flow paths explicitly across the groundwater catchment. Hence, a more distributed, finite-difference modelling approach using MODFLOW Unstructured Grid (USG) with the newly developed Connected Linear Network (CLN) process is then compared against the semidistributed approach on the same karst catchment. Whilst it has proven difficult to achieve the same levels of model performance in simulating the spring flows in the distributed model compared to the semidistributed model, the ability to interrogate the flow paths at any point on the three-dimensional aquifer is demonstrated, which can give new insights into flows (and potential contaminant transport) through such complex systems. The influence of the proximity of highly transmissive conduits on the flow dynamics through the much-lower transmissive matrix cells in which the network is embedded has been particularly investigated.
An algorithm is presented for the detection of frequency contour sounds-whistles of dolphins and many other odontocetes, moans of baleen whales, chirps of birds, and numerous other animal and ...non-animal sounds. The algorithm works by tracking spectral peaks over time, grouping together peaks in successive time slices in a spectrogram if the peaks are sufficiently near in frequency and form a smooth contour over time. The algorithm has nine parameters, including the ones needed for spectrogram calculation and normalization. Finding optimal values for all of these parameters simultaneously requires a search of parameter space, and a grid search technique is described. The frequency contour detection method and parameter optimization technique are applied to the problem of detecting "boing" sounds of minke whales from near Hawaii. The test data set contained many humpback whale sounds in the frequency range of interest. Detection performance is quantified, and the method is found to work well at detecting boings, with a false-detection rate of 3% for the target missed-call rate of 25%. It has also worked well anecdotally for other marine and some terrestrial species, and could be applied to any species that produces a frequency contour, or to non-animal sounds as well.
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