Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Effects of fermentation residues on the melt processability and thermomechanical degradation of PHBV produced from cheese whey using mixed microbial cultures

"Available online 28 March 2016"

Sensitive label-free electron chemical capacitive transducer signal for D-dimer electroanalyses

Supplementary data associated with this article can be found, in the online version, at: http://dx.doi.org/10.1016/j.electacta.2015.09.169.

Anti-inflammatory and antinociceptive activities of Bauhinia monandra leaf lectin

A galactose-specific lectin from Bauhinia monandra leaves (BmoLL) have been purified through ammonium sulphate fractionation followed by guar gel affinity chromatography column. This study aimed to evaluate the potential anti-inflammatory and antinociceptive activity of pure BmoLL in mice. Anti-inflammatory activity was evaluated by 1% carrageenan-induced inflammation in mice treated with BmoLL. Acetic acid-induced abdominal writhing and hot plate methods evaluated antinociceptive activity. BmoLL significantly inhibited the carrageenan-induced paw edema by 47% (30 mg/kg) and 60.5% (60 mg/kg); acetylsalicylic acid (ASA, 100 mg/kg) showed inhibition of 70.5%, in comparison to controls. Leukocyte migration, an immune response to the inflammation process, was significantly reduced in presence of BmoLL; in mice treated with \ASA\ the decrease in leukocyte migration was similar to 15 mg/kg of the lectin. BmoLL at doses of 15, 30 and 60 mg/kg significantly reduced the number of animal contortions by 43.1, 50.1 and 71.3%, respectively.BmoLL leukocyte migration was significantly reduced; in mice treated with \ASA\ the decrease in leukocyte migration was similar to 15 mg/kg of the lectin. BmoLL at doses of 15, 30 and 60 mg/kg significantly reduced the number of animal contortions by 43.1, 50.1 and 71.3%, respectively. The lectin (30 and 60 mg/kg) showed a significant effect in the hot plate assay. BmoLL anti-inflammatory and antinociceptive effects were dose-dependent. The search for new and natural compounds, with minimal side effects, to control pain and inflammation, is constantly increasing. BmoLL has great potential as a natural anti-inflamatory product that can be explored for pharmacological purposes.

Laccase immobilization on bacterial nanocellulose membranes: antimicrobial, kinetic and stability properties

This work studied the physical immobilization of a commercial laccase on bacterial nanocellulose (BNC) aiming to identify the laccase antibacterial properties suitable for wound dressings. Physico-chemical analysis demonstrates that the BNC structure is manly formed by pure crystalline I cellulose. The pH optimum and activation energy of free laccase depends on the substrate employed corresponding to pH 6, 7, 3 and 57, 22, 48 kJ mol1 for 2,6-dimethylphenol (DMP), catechol and 2,2 -azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), respectively. The Michaelis-Menten constant (Km) value for the immobilized laccase (0.77 mM) was found to be almost double of that of the free enzyme (0.42 mM). However, the specific activities of immobilized and free laccase are similar suggesting that the cage-like structure of BNC allows entrapped laccase to maintain some flexibility and favour substrate accessibility. The results clearly show the antimicrobial effect of laccase in Gram-positive (92%) and Gram-negative (26%) bacteria and cytotoxicity acceptable for wound dressing applications.

Bacterial cellulose-lactoferrin as an antimicrobial edible packaging

Bacterial cellulose (BC) films from two distinct sources (obtained by static culture with Gluconacetobacter xylinus ATCC 53582 (BC1) and from a commercial source (BC2)) were modified by bovine lactoferrin (bLF) adsorption. The functionalized films (BC+bLF) were assessed as edible antimicrobial packaging, for use in direct contact with highly perishable foods, specifically fresh sausage as a model of meat products. BC+bLF films and sausage casings were characterized regarding their water vapour permeability (WVP), mechanical properties, and bactericidal efficiency against two food pathogens, Escherichia coli and Staphylococcus aureus. Considering their edibility, an in vitro gastrointestinal tract model was used to study the changes occurring in the BC films during passage through the gastrointestinal tract. Moreover, the cytotoxicity of the BC films against 3T3 mouse embryo fibroblasts was evaluated. BC1 and BC2 showed equivalent density, WVP and maximum tensile strength. The percentage of bactericidal efficiency of BC1 and BC2 with adsorbed bLF (BC1+bLF and BC2+bLF, respectively) in the standalone films and in inoculated fresh sausages, was similar against E. coli (mean reduction 69 % in the films per se versus 94 % in the sausages) and S. aureus (mean reduction 97 % in the films per se versus 36 % in the case sausages). Moreover, the BC1+bLF and BC2+bLF films significantly hindered the specific growth rate of both bacteria. Finally, no relevant cytotoxicity against 3T3 fibroblasts was found for the films before and after the simulated digestion. BC films with adsorbed bLF may constitute an approach in the development of bio-based edible antimicrobial packaging systems.

Production of whey protein-based aggregates under ohmic heating

Formation of whey protein isolate protein aggregates under the influence of moderate electric fields upon ohmic heating (OH) has been monitored through evaluation of molecular protein unfolding, loss of its solubility, and aggregation. To shed more light on the microstructure of the protein aggregates produced by OH, samples were assayed by transmission electron microscopy (TEM). Results show that during early steps of an OH thermal treatment, aggregation of whey proteins can be reduced with a concomitant reduction of the heating chargeby reducing the come-up time (CUT) needed to reach a target temperatureand increase of the electric field applied (from 6 to 12 V cm1). Exposure of reactive free thiol groups involved in molecular unfolding of -lactoglobulin (-lg) can be reduced from 10 to 20 %, when a CUT of 10 s is combined with an electric field of 12 V cm1. Kinetic and multivariate analysis evidenced that the presence of an electric field during heating contributes to a change in the amplitude of aggregation, as well as in the shape of the produced aggregates. TEM discloses the appearance of small fibrillar aggregates upon the influence of OH, which have recognized potential in the functionalization of food protein networks. This study demonstrated that OH technology can be used to tailor denaturation and aggregation behavior of whey proteins due to the presence of a constant electric field together with the ability to provide a very fast heating, thus overcoming heat transfer limitations that naturally occur during conventional thermal treatments.

Factors associated with willingness to donate embryos for research among couples undergoing IVF

Between 2011 and 2012, 213 heterosexual couples undergoing fertility treatments in a Portuguese public fertility centre were systematically recruited to assess factors associated with willingness to donate embryos for research. Data were collected by questionnaire. Most couples (87.3%; 95% CI 82.1 to 91.5) were willing to donate embryos for research, citing benefits for science, health and infertile patients. Almost all couples (94.3%; 95% CI 89.8 to 96.7) reached consensus about the decision. Willingness to donate was more frequent in women younger than 36 years (adjusted OR 3.06; 95% CI 1.23 to 7.61) and who considered embryo research to be very important (adjusted OR: 6.32; 95% CI 1.85 to 21.64), and in Catholic men (adjusted OR 4.16; 95% CI 1.53 to 11.30). Those unwilling to donate reported conceptualizing embryos as children or living beings and a lack of information or fears about embryo research. Men with higher levels of trait anxiety (adjusted OR 0.90; 95% CI 0.84 to 0.96) were less frequently willing to donate. Future research on embryo disposition decision-making should include the assessment of gender differences and psychosocial factors. Ethically robust policies and accurate information about the results of human embryo research are required.

Couple's willingness to donate embryos for research: a longitudinal study

Introduction. Decision-making on embryo disposition is a source of distress and is subject to change over time. This paper analyses the willingness of couples undergoing in vitro fertilization to donate cryopreserved embryos for research from 15 days after embryo transfer to 12 months later, taking into account the influence of psychosocial, demographic, and reproductive factors. Materials and methods. Prospective longitudinal study, with 74 heterosexual couples undergoing in vitro fertilization in a public fertility centre in Portugal, recruited between 2011 and 2012. Participants were evaluated twice: 15 days after embryo transfer and 12 months later. Results. A significant decrease in patients’ willingness to donate embryos for research over time was observed [86.5% to 73.6%; relative risk (RR) = 0.85; 95% CI 0.76–0.95]. A higher education level (>12 years) [adjusted RR (RRadj) = 0.79; 95% CI 0.64–0.96], considering research on human embryos to be important (vs. very important) (RRadj = 0.59; 95% CI 0.39–0.85) and practicing a religion less than once a month (vs. at least once a month) (RRadj = 0.73; 95% CI 0.53–1.00) seemed associated with unwillingness to donate embryos for research over time. Change towards non-donation happened mainly among couples who first considered that it was better to donate than wasting the embryos. Change towards donation occurred mostly among those stating that their priority at time 1 was to have a baby and who became pregnant in the meantime. Conclusions. Quality of care guided by patients’ characteristics, values, preferences, and needs calls for considering the factors and reasons underlying couples’ willingness to donate embryos for research over time as a topic in psychosocial guidelines for infertility and medically assisted reproductive care.

Self-reported psychosocial factors among In Vitro Fertilization patients interviewed alone or with the partner

"Published online: 07 Nov 2015"

Partner relationships during pregnancy in anxious and depressed women and men

To assess anxiety, depression and relationship satisfaction in both women and men during pregnancy, the State Anxiety Inventory (STAI), The Center for Epidemiological Studies-Depression Scale (CES-D) and The Relationship Questionnaire (RQ) were administered during the second trimester to a sample of 59 pregnant women and their partners. Anxious pregnant women rated their relationships as less positive. Depressed pregnant women also rated their relationships as less positive. The women’s anxiety scores were predictive of their positive and negative relationship scores. The women and their partners’ negative relationship scores were also predictive of each others’ negative relationship scores. These results highlight the importance of targeting anxiety as well as depression, and pregnant women as well as their partners in prenatal intervention programs.

A comparative study in two secondary schools aimed at improving their energy management: Archbishop McHale College Tuam, Coláiste Cholmcille Indreabhánn

Climate change is a crisis that is going to affect all of our lives in the future. Ireland is expected to have increased storms and rain throughout the country. This will affect our lives greatly unless we do something to change it. In an attempt to try and reduce the impacts of climate change, countries across the world met to address the problem. The meeting became known as the Kyoto Protocol. The Kyoto protocol set out objectives for each developed country to achieve with regards to carbon emissions to the same levels as 1990 levels. Due to the economy in Ireland being at a low point in 1990, Ireland was given a target of 13% carbon emissions above 1990 levels. In order to meet targets Ireland produced two energy papers, the green paper and the white paper. The green paper identified drivers for energy management and control; they were security of energy supply, economic competitiveness and environmental protection. The white paper produced targets in which we should aim to achieve to try and address the green papers drivers. Within the targets was the plan to reduce energy consumption in the public sector by 33% by 2020 through energy conservation measures. Schools are part of the public sector that has targets to reduce its energy consumption. To help to achieve targets in schools initiatives have been developed by the government for schools. Energy audits should be performed in order to identify areas where the schools can improve their current trends and show where they can invest in the future to save money and reduce the schools overall environmental footprint. Grants are available for the schools for insulation through the energy efficiency scheme and for renewable energy technologies through the ReHeat scheme. The promotion of energy efficient programs in schools can have a positive effect for students to have an understanding. The Display Energy Certificate is a legal document that can be used to understand how each school is performing from an energy perspective. It can help schools to understand why they need to change their current energy management structure. By improving the energy management of the schools they then improve the performance on the Display Energy Certificate. Schools should use these tools wisely and take advantage of the grants available which can in the short to long term help them to save money and reduce their carbon footprint.

Development of an integrated approach to reliability management and operation

The research described in this thesis has been developed as a part of the Reliability and Field Data Management for Multi-component Products (REFIDAM) Project. This project was founded under the Applied Research Grants Scheme administered by Enterprise Ireland. The project was a partnership between Galway-Mayo Institute of Technology and Thermo King Europe. The project aimed to develop a system in order to manage the information required for reliability assessment and improvement of multi-component products, by establishing information flows within the company and information exchange with fleet users.

Development of a life cycle management system for remote products.

The research described in this thesis has been developed as a part of the Reliability and Field Data Management for Multi-Component Products (REFIDAM) Project. This project was funded under the Applied Research Grants Scheme administered by Enterprise Ireland. The project was a partnership between Galway-Mayo Institute of Technology and an industrial company, Thermo King Europe. The project aimed to develop a system to manage the information required for maintenance costing, cost of ownership, reliability assessment and improvement of multi-component products, by establishing information flows between the customer network and across the Thermo King organisation.

Implementation of a customer relationship management system in an SME

The research conducted for this thesis has been carried out over a two year period as part of the Mobile Tools and Technology for customer care (MOTTO) project. The project was funded under the Applied Grant scheme administered by Enterprise Ireland and Nortel Networks Ltd. It was a partnership project between Galway-Mayo Institute of Technology, University of Limerick, National University of Ireland Galway, and a global Internet and communications company, Nortel Networks. The project aimed to investigate the enabling mobile communications technologies in e-Business and mobile communications in the area of Business-to-Business (B2B) customer care. The development of the application discussed in this thesis was developed in conjunction with the Galway-Mayo Institute of Technology, University of Limerick and AMT Ireland. The decision to develop the application in the Electronics Company of AMT in Limerick came about as a result of the contact established by Mark Southern from the University of Limerick. Mark was involved in overseeing the development and assisted in establishing the user requirements.