Model reduction of genome-scale metabolic models as a basis for targeted kinetic models.

Constraint-based, genome-scale metabolic models are an essential tool to guide metabolic engineering. However, they lack the detail and time dimension that kinetic models with enzyme dynamics offer. Model reduction can be used to bridge the gap between the two methods and allow for the integration of kinetic models into the Design-Built-Test-Learn cycle. Here we show that these reduced size models can be representative of the dynamics of the original model and demonstrate the automated generation and parameterisation of such models. Using these minimal models of metabolism could allow for further exploration of dynamic responses in metabolic networks.

Necrotizing soft tissue infections - a multicentre, prospective observational study (INFECT): protocol and statistical analysis plan.

BACKGROUND: The INFECT project aims to advance our understanding of the pathophysiological mechanisms in necrotizing soft tissue infections (NSTIs). The INFECT observational study is part of the INFECT project with the aim of studying the clinical profile of patients with NSTIs and correlating these to patient-important outcomes. With this protocol and statistical analysis plan we describe the methods used to obtain data and the details of the planned analyses. METHODS: The INFECT study is a multicentre, prospective observational cohort study. Patients with NSTIs are enrolled in five Scandinavian hospitals, which are all referral centres for NSTIs. The primary outcomes are the descriptive variables of the patients. Secondary outcomes include identification of factors associated with 90-day mortality and amputation; associations between affected body part, maximum skin defect and Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC) score and 90-day mortality; 90-day mortality in patients with and without acute kidney injury (AKI) and LRINEC score of six and above or below six; and association between affected body part at arrival and microbiological findings. Exploratory outcomes include univariate analyses of baseline characteristics associations with 90-day mortality. The statistical analyses will be conducted in accordance with the predefined statistical analysis plan. CONCLUSION: Necrotizing soft tissue infections result in severe morbidity and mortality. The INFECT study will be the largest prospective study in patients with NSTIs to date and will provide important data for clinicians, researchers and policy makers on the characteristics and outcomes of these patients.

Spectrophotometric Analysis of Apical Extrusion of Sodium Hypochlorite using Different Irrigation Protocols in an Ex Vivo Model of Immature Teeth.

OBJECTIVE: To evaluate the effect of different agitation methods on apical extrusion of 1.5% sodium hypochlorite (NaOCl) in an ex vivo model of immature teeth. METHODS: Sixty extracted human inferior incisors were prepared to simulate immature teeth and embedded in an artificial root socket made of silicone impression material. The teeth were then divided into four groups: Conventional needle irrigation (CNI) alone, CNI supplemented with Ultrasonic Irrigant Activation (UIA), EasyClean (EC), or XP-endo Finisher (XPF). Extruded NaOCl was collected, reacted with m-cresol purple, and its absorbance values were measured. The data were statistically analyzed using One-way analysis of variance with a significance level of 5%. RESULTS: All groups showed apically extruded irrigating solution, and the mean volumes of extruded NaOCl did not differ significantly between any of the test groups (p⟩0.05). CONCLUSION: The activation of 1.5% NaOCL by UIA, EC, or XPF as supplementary to CNI does not promote greater apical extrusion when compared to CNI alone in simulated immature teeth.

A limited LCA of bio-adipic acid: manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks.

A limited life cycle assessment (LCA) was performed on a combined biological and chemical process for the production of adipic acid, which was compared to the traditional petrochemical process. The LCA comprises the biological conversion of the aromatic feedstocks benzoic acid, impure aromatics, toluene, or phenol from lignin to cis, cis-muconic acid, which is subsequently converted to adipic acid through hydrogenation. Apart from the impact of usage of petrochemical and biomass-based feedstocks, the environmental impact of the final concentration of cis, cis-muconic acid in the fermentation broth was studied using 1.85% and 4.26% cis, cis-muconic acid. The LCA focused on the cumulative energy demand (CED), cumulative exergy demand (CExD), and the CO(2) equivalent (CO(2) eq) emission, with CO(2) and N(2) O measured separately. The highest calculated reduction potential of CED and CExD were achieved using phenol, which reduced the CED by 29% and 57% with 1.85% and 4.26% cis, cis-muconic acid, respectively. A decrease in the CO(2) eq emission was especially achieved when the N(2) O emission in the combined biological and chemical process was restricted. At 4.26% cis, cis-muconic acid, the different carbon backbone feedstocks contributed to an optimized reduction of CO(2) eq emissions ranging from 14.0 to 17.4 ton CO(2) eq/ton adipic acid. The bulk of the bioprocessing energy intensity is attributed to the hydrogenation reactor, which has a high environmental impact and a direct relationship with the product concentration in the broth.

Herbivory and leaf traits of Amazonian tree species as affected by irradiance.

Herbivory is one of the major biotic stress factors that affect the establishment of plants. However, the main factors that drive herbivory in seedlings of Amazonian tree species are still not well understood. Here we investigated whether contrasting levels of irradiance influence herbivory according to different herbivory indicators and which leaf traits are most related to interspecific variation in herbivory under contrasting irradiance conditions. We measured the leaf area lost as a result of insect herbivory in five tree species planted in a silvicultural system of secondary forest enrichment according to two indicators, herbivore damage (accumulated since plant germination) and herbivory rate (measured over time), and two irradiance conditions, understorey PPFD 2.6 mol·m-2 ·day-1 ) and gap PPFD 33.1 mol·m-2 ·day-1 . Furthermore, we related the interspecific variation in herbivory to a set of leaf traits: SLA, RWC, sclerophylly, phenolic compound content, tannins, condensed tannins and non-structural carbohydrates. Herbivore damage was significantly affected by light availability and species, with the highest percentage variation observed in the Meliaceae (Carapa guianensis and Swietenia macrophylla). For the herbivory rate, only the interspecific variation was significant, with Bertholletia excelsa having the lowest rates. Chemical characteristics (phenolic compounds and tannins) were most related to herbivory rates, as well as highly influenced by light conditions. Non-structural carbohydrates (starch and sucrose) were also related to the interspecific variation in herbivory. The phenolic compounds and starch, as affected by light quantity, are species dependent. Thus, the selective pressure on herbivores may be driven by species-dependent responses to light conditions.

Draft Genome Sequence of the Oleaginous Green Alga Tetradesmus obliquus UTEX 393.

The microalgae Tetradesmus obliquus is able to maintain a high photosynthetic efficiency under nitrogen limitation and is considered a promising green microalgae for sustainable production of diverse compounds, including biofuels. Here, we report the first draft whole-genome shotgun sequencing of T. obliquus The final assembly comprises 108,715,903 bp with over 1,368 scaffolds.

Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters.

BACKGROUND: The development of biological processes that replace the existing petrochemical-based industry is one of the biggest challenges in biotechnology. Aspergillus niger is one of the main industrial producers of lignocellulolytic enzymes, which are used in the conversion of lignocellulosic feedstocks into fermentable sugars. Both the hydrolytic enzymes responsible for lignocellulose depolymerisation and the molecular mechanisms controlling their expression have been well described, but little is known about the transport systems for sugar uptake in A. niger. Understanding the transportome of A. niger is essential to achieve further improvements at strain and process design level. Therefore, this study aims to identify and classify A. niger sugar transporters, using newly developed tools for in silico and in vivo analysis of its membrane-associated proteome. RESULTS: In the present research work, a hidden Markov model (HMM), that shows a good performance in the identification and segmentation of functionally validated glucose transporters, was constructed. The model (HMMgluT) was used to analyse the A. niger membrane-associated proteome response to high and low glucose concentrations at a low pH. By combining the abundance patterns of the proteins found in the A. niger plasmalemma proteome with their HMMgluT scores, two new putative high-affinity glucose transporters, denoted MstG and MstH, were identified. MstG and MstH were functionally validated and biochemically characterised by heterologous expression in a S. cerevisiae glucose transport null mutant. They were shown to be a high-affinity glucose transporter (K m = 0.5 ± 0.04 mM) and a very high-affinity glucose transporter (K m = 0.06 ± 0.005 mM), respectively. CONCLUSIONS: This study, focusing for the first time on the membrane-associated proteome of the industrially relevant organism A. niger, shows the global response of the transportome to the availability of different glucose concentrations. Analysis of the A. niger transportome with the newly developed HMMgluT showed to be an efficient approach for the identification and classification of new glucose transporters.

Serodiagnosis of hepatitis C virus. Effect of new evaluation of cutoff values for enzyme-linked immunosorbent assay in Brazilian patients.

With the goal of reducing false-positive results in enzyme-linked immunosorbent assay (ELISA) serodiagnosis of hepatitis C virus in clinical practice, a study was undertaken to establish better cutoff values. We examined 277 serum samples from patients with hepatitis (non-A, non-B; B; autoimmune); subjects with antinuclear antibodies or rheumatoid factor, anticytomegalovirus or Epstein-Barr virus IgG or IgM antibodies, or parasitic disease (Chagas disease, leishmaniasis); and healthy volunteers. Concordant positive results in 2 different immunoblot assays in 250 samples were taken as indicative of true-positive, and when negative, of absence of infection. Reactivity in 3 ELISA tests were evaluated for the manufacturer recommended cutoff (CO) and for 2CO, 3CO, and 4CO; and corresponding sensitivity and specificity were calculated for single or combined pairs of ELISA tests. Although CO is adequate for blood bank screening, because it provides maximal sensitivity, the frequently observed false-positive results could be significantly reduced by increasing the cutoff value to 2CO, with no significant loss in sensitivity either in relation to pairs of immunoenzymatic tests or to a single ELISA.

Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield.

Pseudomonas putida KT2440-JD1 was derived from P. putida KT2440 after N-methyl-N'-nitro-N-nitrosoguanidine (NTG)-mutagenesis and exposure to 3-fluorobenzoate (3-FB). The mutant was no longer able to grow using benzoate as a sole carbon source, but co-metabolized benzoate to cis, cis-muconate during growth on glucose, which accumulated in the growth medium. The specific production rate (q(pm)) was 0.18±0.03 g cis, cis-muconate/(g(DCW) h) in continuous cultures, and increased to 1.4 g cis, cis-muconate/(g(DCW) h) during wash-out cultivation. Transcriptome analysis showed that the cat operon was not induced in P. putida KT2440-JD1 in the presence of 5mM benzoate, due to a point mutation in the highly conserved DNA binding domain of the transcriptional regulator (catR) of the cat operon. The ben operon was highly expressed in the presence of benzoate in the mutant and its parental strain. This operon contains PP_3166 (catA2), which was shown to be a second catechol 1,2-dioxygenase besides catA. P. putida KT2440-JD1 is the first cis, cis-muconate-accumulating mutant that was characterized at the genetic level. The specific production rate achieved is at least eight times higher than those reported for other cis, cis-muconate-producing strains.

Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440.

A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.

Relevance of rheological properties of gel beads for their mechanical stability in bioreactors.

The mechanical stability of biocatalyst particles in bioreactors is of crucial importance for applications of immobilized-cell technology in bioconversions. The common methods for evaluation of the strength of polymer beads (mostly force-to-fracture or tensile tests) are, however, not yet proven to be relevant for the assessment of their mechanical stability in bioreactors. Therefore, we tested fracture properties of gel materials and investigated their relevance for abrasion in bioreactors. Abrasion of gel beads was assumed to be a continuous fracturing of the bead surface. At first, three rheological properties were considered: stress at fracture; strain at fracture; and the total fracture energy. If stress at fracture is the most important property, beads having a similar fracture energy, but a smaller stress at fracture, would abrade faster in a bioreactor than beads with a larger stress at fracture; if fracture energy the determining factor, beads that require less energy to fracture would abrade faster than those having a larger fracture energy for the same fracture stress. To determine this, beads of kappa-carrageenan and agar (at two different polymer concentrations) were tested for abrasion in four identical bubble columns under the same operating conditions. Agar beads were expected to abrade faster than those of carrageenan because agar had either a lower stress at fracture or a lower fracture energy. However, no correlation between fracture properties and abrasion rate was found in any of the combinations tested. Carrageenan beads abraded faster than those of agar in all combinations. Furthermore, both the stress and strain at fracture of agar and carrageenan beads decreased during the run and those of carrageenan decreased faster, suggesting that the gels are liable to fatigue in different ways. This hypothesis was confirmed by oscillating experiments in which gel samples were subjected to repeated compressions below their fracture levels. Their resistance to compression clearly decreased with the number of oscillations. Fatigue is probably related to the development of microcracks and microfracture propagation within the material. We concluded that: (a) the use of tests based on bead rupture do not provide relevant information on the mechanical stability of gel beads to abrasion; and (b) abrasion of polymer beads is likely to be related to fatigue of the gel materials. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 517-529, 1997.

Kinetics and performance of a co-immobilised system of amyloglucosidase and Zymomonas mobilis.

High operational stability and productivity of co-immobilised systems are important aspects for their successful application in industrial processes. A dynamic model is required to describe artificially co-immobilised systems because the time needed to reach steady state normally exceeds the operational life span of these systems. Time dependent intraparticle concentration profiles and macroscopic conversion were modelled to study the operational stability and productivity of these systems theoretically. The model was used to describe experimental results of ethanol production from maltose by a co-immobilised system of amyloglucosidase and Zymomonas mobilis. Furthermore, the influence of the immobilisation procedure with glutaraldehyde and polyethyleneimine could also be studied with and incorporated in the model. From the model it could be derived that co-immobilised systems performing a consecutive reaction evolve towards a steady state, characterised by a constant concentration of the intermediate in the particle if product inhibition is neglected. Such a situation develops independently of the biomass concentration and the radial position, and has important consequences for co-immobilised systems. When the concentration of the intermediate in the bulk liquid is lower than this constant value in the biocatalyst particle, two regions may be distinguished in the particle: an inactive peripheral region without biomass and an active core with a biomass concentration depending on the substrate and immobilised enzyme concentration. Unlike immobilised single cell systems, it is possible to obtain a real steady state and therefore a stable situation for co-immobilised systems. However, a high operational life time could only be achieved at the expense of the productivity of the biocatalyst particle. A stability criterion is derived which agrees very well with the simulation results.

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.