110 research outputs found
The Sponge RNAs of bacteria - How to find them and their role in regulating the post-transcriptional network
No full textIn bacteria small regulatory RNAs (sRNAs) interact with their mRNA targets through non-consecutive base-pairing. The loose base-pairing specificity allows sRNAs to regulate large numbers of genes, either affecting the stability and/or the translation of mRNAs. Mechanisms enabling post-transcriptional regulation of the sRNAs themselves have also been described involving so-called sponge RNAs. Sponge RNAs modulate free sRNA levels in the cell through RNA-RNA interactions that sequester ("soak up") the sRNA and/or promote degradation of the target sRNA or the sponge RNA-sRNA complex. The development of complex RNA sequencing strategies for the detection of RNA-RNA interactions has enabled identification of several sponge RNAs, as well as previously known regulatory RNAs able to act as both regulators and sponges. This review highlights techniques that have enabled the identification of these sponge RNAs, the origins of sponge RNAs and the mechanisms by which they function in the post-transcriptional network.</p
The political economy of trade and growth: an analytical interpretation of sir James Steuart's inquiry
No full textSir James Steuart (1713-80) has been unduly neglected by the majority of historians of economic thought. This study aims at casting a new light upon his original thought to provide a basis for the revaluation of his contribution to the development of economic discipline. The present interpretation of his Inquiry (1767) reveals that his political economy contains not only fresh new ideas and path-breaking thinking for his time but also most major ingredients of modem economics. Firmly based on the recognition of the interdependence of economic sectors and social classes, he clearly grasped the circular system of production, distribution and consumption in the exchange economy. He discerned between the 'profit upon alienation' and the 'real value' of commodities in their current price' determined in the markets. He emphasized the 'balance of work and demand', secured by the 'double competition' among the sellers and buyers of commodities, for the efficient allocation of economic resources. On these foundations, Steuart established his theory of output, employment and population in terms of the notion of 'effectual demand'. His economic analysis culminates in his discussions of economic growth and foreign trade. He linked the limitations of the former to the benefits of the latter. Meanwhile, refuting his predecessors' quantity theory, Steuart presented what might be called the production-consumption theory of money, according to which money is not neutral to the determination of the level of output in an exchange economy. His theory of international money also takes on modernity, as it adopts an absorption approach to the balance of payments. Steuart's monetary analysis comes complete with his argument for government's active finance. The state interventionism underlying the whole of Steuart's political economy is seen as its logical conclusion, rather than a mere assumption. Thus, it is suggested that the ultimate message of his Inquiry is neither laissez faire nor centa-al planning
γ-PGA production through Consolidated Bioprocessing in engineered B. subtilis lab strains
No full textPoly-γ-glutamic acid (γ-PGA) is a nontoxic, biodegradable, highly anionic homo-polyamide formed by multiple repetitions of D-/L- glutamic acid units polymerized by amide linkages between the α-NH2 and γ-COOH groups. The polymer is endowed with several favorable characteristics and has been exploited in a growing number of biotechnological applications. Moreover, ground-breaking γ-PGA applications in the biomedical field, as drug carrier, gene delivery and scaffold for tissue engineering are currently under investigation.
The RiVaRIO project is focused on reducing γ-PGA fermentation costs through the exploitation of one of the most abundant biomass resources - rice straw - as unique feedstock in aerobic fermentation. First, a cheap and scalable straw pretreatment was identified that dramatically improves the saccharification efficiency of the lignocellulose matrix. Next, the cellulolytic capabilities of a B. subtilis JH642 were maximized by self-cloning procedures. The efficient growth of B. subtilis on treated straw will be presented.
Furthermore, by transferring the cellulolytic modifications in a high-yield γ-PGA producer strain, direct production of γ-PGA from biomass fermentation could be obtained, proving the applicability of Consolidated Bioprocessing concepts to B. subtilis
Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression
No full textBacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5= untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNAmediated gene regulation in B. subtilis mostly involves elements at the 5= ends of mRNA molecules. These can include 5= secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis
Phenol-soluble modulins, hellhounds from the staphylococcal virulence-factor pandemonium
No full textPhenol-soluble modulins are secreted peptides with multiple functions in Staphylococcus aureus pathogenesis and spreading. Recent studies by Otto and coworkers show that these hellhounds of the staphylococcal virulence-factor pandemonium are unleashed through an essential ABC transporter, which represents an exciting new target for stopping the spread of this important pathogen
Development and application of a LC-MS/MS assay for simultaneous analysis of 25-hydroxyvitamin-D and 3-epi-25-hydroxyvitamin-D metabolites in canine serum
No full textHypovitaminosis D and hypervitaminosis D are well recognised disorders in dogs. Hypovitaminosis D can occur following consumption of a diet inadequately supplemented with vitamin D or as a sequelae of severe intestinal disease. Hypervitaminosis D may occur as a result of consuming proprietary dog foods over-supplemented with vitamin D or through ingestion of vitamin D containing medicinal products or rodenticides. Consequently, there is a clear need to establish a methodology that can accurately quantify vitamin D metabolites across a broad dynamic range in dogs. The existence of C3-epimers of vitamin D metabolites has yet to be elucidated in dogs, yet are known to interfere with the analysis of vitamin D and have unknown biological activity in other species. Here, we describe the development and validation of a sensitive, specific and robust analytical liquid chromatography tandem mass spectrometry (LC-MS/MS) assay capable of separating and accurately measuring 25-hydroxyvitamin-D2/3 (25(OH)D2/3) and 3-epi-25-hydroxyvitamin-D2/3 (3-epi-25(OH)D2/3). We describe a simplified workflow utilising supported liquid extraction (SLE) without derivatization that provides good linearity (mean r > 0.996) and accuracy across a broad dynamic range of 4-500 nmol/L for D3 metabolites and 7.8-500 nmol/L for D2 metabolites. Upon application of this assay to 117 canine serum samples, 25(OH)D3 was detectable in all samples with a median concentration of 82.1 nmol/L (inter-quartile range (IQR) 59.7-101.8 nmol/L). 3-epi-25(OH)D3 could be detected in 87.2 % of the study population, with a median concentration of 5.2 nmol/L (2.4-8.1 nmol/L). However, 3-epi-25(OH)D3 was quantified below the LLOQ in 40.2 % of these samples. 3-epi-25(OH)D3 contributed on average 6.3 % to 25(OH)D3 status (contribution ranges from 0 to 23.8%) and a positive correlation was detected between 25(OH)D3 and 3-epi-25(OH)D3 concentrations. Free 25(OH)D was also measured using an immunoassay with a median concentration of 15.2 pmol/L (12.5-23.2 pmol/L), and this metabolite was also positively correlated to both 3-epi-25(OH)D3 and 25(OH)D3 concentrations. D2 metabolites were not detected in canine serum as expected. Vitamin D metabolite concentrations were variable between individuals, and research into the causes of this variation should include factors such as breed, age, sex and neuter status to determine the impact of genetic and hormonal factors. Given the clinical importance of vitamin D in dogs, and the immense potential for utilising this species as a model for human disease, further elucidation of the vitamin D pathway in this species would provide immense clinical and research benefit
Embryonic and induced pluripotent stem cells: understanding, creating, and exploiting the nano-niche for regenerative medicine.
No full textEmbryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have the capacity to differentiate into any specialized cell type of the human body, and therefore, ESC/iPSC-derived cell types offer great potential for regenerative medicine. However, key to realizing this potential requires a strong understanding of stem cell biology, techniques to maintain stem cells, and strategies to manipulate cells to efficiently direct cell differentiation toward a desired cell type. As nanoscale science and engineering continues to produce novel nanotechnology platforms, which inform, infiltrate, and impinge on many aspects of everyday life, it is no surprise that stem cell research is turning toward developments in nanotechnology to answer research questions and to overcome obstacles in regenerative medicine. Here we discuss recent advances in ESC and iPSC manipulation using nanomaterials and highlight future challenges within this area of research
The reduction in small ribosomal subunit abundance in ethanol-stressed cells of Bacillus subtilis is mediated by a SigB-dependent antisense RNA
No full textOne of the best-characterized general stress responses in bacteria is the σB-mediated stress response of the Gram-positive soil bacterium Bacillus subtilis. The σB regulon contains approximately 200 protein-encoding genes and 136 putative regulatory RNAs. One of these σB-dependent RNAs, named S1136–S1134, was recently mapped as being transcribed from the S1136 promoter on the opposite strand of the essential rpsD gene, which encodes the ribosomal primary-binding protein S4. Accordingly, S1136–S1134 transcription results in an rpsD-overlapping antisense RNA (asRNA). Upon exposure of B. subtilis to ethanol, the S1136 promoter was found to be induced, while rpsD transcription was downregulated. By quantitative PCR, we show that the activation of transcription from the S1136 promoter is directly responsible for the downregulation of rpsD upon ethanol exposure. We also show that this downregulation of rpsD leads to a reduced level of the small (30S) ribosomal subunit upon ethanol stress. The activation of the S1136 promoter thus represents the first example of antisense transcription-mediated regulation in the general stress response of B. subtilis and implicates the reduction of ribosomal protein abundance as a new aspect in the σB-dependent stress response. We propose that the observed reduction in the level of the small ribosomal subunit, which contains the ribosome-decoding center, may protect B. subtilis cells against misreading and spurious translation of possibly toxic aberrant peptides under conditions of ethanol stress
The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism
No full textExpression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health. To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis. By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis. Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge. We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures. These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription. Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide. Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter
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