Isothermal micro calorimetry - a new method for MIC determinations: results for 12 antibiotics and reference strains of E. coli and S. aureus

Background  

Antimicrobial susceptibility testing of microorganisms is performed by either disc diffusion or broth dilution tests. In clinical use, the tests are often still performed manually although automated systems exist. Most systems, however, are based on turbidometric methods which have well-known drawbacks.     

Transcriptome profiling of a curdlan-producing <Emphasis Type="Italic">Agrobacterium</Emphasis> reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis

Background  

The ability to synthesize exopolysaccharides (EPS) is widespread among microorganisms, and microbial EPS play important roles in biofilm formation, pathogen persistence, and applications in the food and medical industries. Although it is well established that EPS synthesis is invariably in response to environmental cues, it remains largely unknown how various environmental signals trigger activation of the biochemical synthesis machinery.     

Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus

Background  

RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans.     

Characterization of the iron-regulated <Emphasis Type="Italic">desA</Emphasis> promoter of <Emphasis Type="Italic">Streptomyces pilosus</Emphasis> as a system for controlled gene expression in actinomycetes

Background  

The bioavailability of iron is quite low since it is usually present as insoluble complexes. To solve the bioavailability problem microorganisms have developed highly efficient iron-scavenging systems based on the synthesis of siderophores that have high iron affinity. The systems of iron assimilation in microorganisms are strictly regulated to control the intracellular iron levels since at high concentrations iron is toxic for cells. Streptomyces pilosus synthesizes the siderofore desferrioxamine B. The first step in desferrioxamine biosynthesis is decarboxylation of L-lysine to form cadaverine, a desferrioxamine B precursor. This reaction is catalyzed by the lysine decarboxylase, an enzyme encoded by the desA gene that is repressed by iron.     

Community-wide analysis of microbial genome sequence signatures

Background  

Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them.     

Effect of modeled reduced gravity conditions on bacterial morphology and physiology

Background  

Bacterial phenotypes result from responses to environmental conditions under which these organisms grow; reduced gravity has been demonstrated in many studies as an environmental condition that profoundly influences microorganisms. In this study, we focused on low-shear stress, modeled reduced gravity (MRG) conditions and examined, for Escherichia coli and Staphlyococcus aureus, a suite of bacterial responses (including total protein concentrations, biovolume, membrane potential and membrane integrity) in rich and dilute media and at exponential and stationary phases for growth. The parameters selected have not been studied in E. coli and S. aureus under MRG conditions and provide critical information about bacterial viability and potential for population growth.     

Environmental life cycle assessment as a tool for identification and assessment of environmental aspects in environmental management systems (EMS) part 1: methodology

Purpose  

The paper presents a discussion on the possibilities of using life cycle assessment (LCA) in identification and assessment of environmental aspects in environmental management systems based on the requirements of the international ISO14001 standard and the European Union EMAS regulation. Some modifications of LCA methodology are proposed in part 1, while the results of a review of environmental aspects for 36 organisations with implemented environmental management systems (EMS) are presented in part 2 of the article.     

Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease

Background  

Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level.     

Environmental life cycle assessment (LCA) as a tool for identification and assessment of environmental aspects in environmental management systems (EMS)

Purpose  

The paper presents a discussion on the possibilities of using LCA in identification and assessment of environmental aspects in environmental management systems based on the requirements of the international ISO14001 standard and the European Union EMAS regulation. Some modifications of LCA methodology are proposed in Part 1 while the results of a review of environmental aspects for 36 organisations with implemented EMS are presented in Part 2 of the article.     

Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration

Background  

Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes.     

An information-flow-based model with dissipation,saturation and direction for active pathway inference

Background  

Biological systems process the genetic information and environmental signals through pathways. How to map the pathways systematically and efficiently from high-throughput genomic and proteomic data is a challenging open problem. Previous methods design different heuristics but do not describe explicitly the behaviours of the information flow.     

designGG: an R-package and web tool for the optimal design of genetical genomics experiments

Background  

High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological systems. The optimal design of such genetical genomics experiments in a cost-efficient and effective way is not trivial.     

OptFlux: an open-source software platform for <Emphasis Type="Italic">in silico</Emphasis> metabolic engineering

Background  

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications.     

Real-time detection of viable microorganisms by intracellular phototautomerism

Background  

To date, the detection of live microorganisms present in the environment or involved in infections is carried out by enumeration of colony forming units on agar plates, which is time consuming, laborious and limited to readily cultivable microorganisms. Although cultivation-independent methods are available, they involve multiple incubation steps and do mostly not discriminate between dead or live microorganisms. We present a novel generic method that is able to specifically monitor living microorganisms in a real-time manner.     

Environmental assessment of sewage effluent disinfection system: electron beam, ultraviolet, and ozone using life cycle assessment

Purpose

This study assesses the impacts of three different disinfection processes of sewage effluent, namely the electron beam (E-beam), ultraviolet (UV), and ozone systems, on the environment by using life cycle assessment (LCA).

Methods

The LCA employed was the comparative LCA which consists of three parts according to life cycle stages. Electricity consumption was the reference flow that can yield 99% disinfection efficiency for microorganisms present in a 1?×?10⁵?m³?day^?1 sewage treatment plant effluent over 20?years.

Results

The comparison of the LCA results indicated that the environmental impact of the UV disinfection system was the lowest, followed by the E-beam and ozone disinfection systems. The key issues of the E-beam, UV, and ozone disinfection systems are electricity consumption and SF₆ usage, electricity consumption and UV lamp, and electricity consumption and liquid oxygen feeding system, respectively.

Conclusions

Electricity consumption is the key input parameter that determines the LCA results.     

Life cycle assessment of soil and groundwater remediation technologies: literature review

Background, aim, and scope  

Life cycle assessment (LCA) is becoming an increasingly widespread tool in support systems for environmental decision-making regarding the cleanup of contaminated sites. In this study, the use of LCA to compare the environmental impacts of different remediation technologies was reviewed. Remediation of a contaminated site reduces a local environmental problem, but at the same time, the remediation activities may cause negative environmental impacts on the local, regional, and global scale. LCA can be used to evaluate the inherent trade-off and to compare remediation scenarios in terms of their associated environmental burden.     

Functional evolution of the trace amine associated receptors in mammals and the loss of TAAR1 in dogs

Background  

The trace amine associated receptor family is a diverse array of GPCRs that arose before the first vertebrates walked on land. Trace amine associated receptor 1 (TAAR1) is a wide spectrum aminergic receptor that acts as a modulator in brain monoaminergic systems. Other trace amine associated receptors appear to relate to environmental perception and show a birth-and-death pattern in mammals similar to olfactory receptors.     

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

Background  

Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning.     

Bacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens

Background  

Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly dependent on agrochemicals. However, intensive use of these compounds has led to the emergence of pathogen resistance and severe negative environmental impacts. There are also a number of plant diseases for which chemical solutions are ineffective or non-existent as well as an increasing demand by consumers for pesticide-free food. Thus, biological control through the use of natural antagonistic microorganisms has emerged as a promising alternative to chemical pesticides for more rational and safe crop management.