Generalizing a hybrid synthetic promoter approach in Yarrowia lipolytica.

Both varied and strong promoters are essential for metabolic and pathway engineering applications in any host organism. To enable this capacity, here we demonstrate a generalizable method for the de novo construction of strong, synthetic hybrid promoter libraries. Specifically, we demonstrate how promoter truncation and fragment dissection analysis can be utilized to identify both novel upstream activating sequences (UAS) and core promoters-the two components required to generate hybrid promoters. As a base case, the native TEF promoter in Yarrowia lipolytica was examined to identify putative UAS elements that serve as modular synthetic transcriptional activators. Resulting synthetic promoters containing a core promoter region activated by between one and twelve tandem repeats of the newly isolated, 230 nucleotide UASTEF#2 element showed promoter strengths 3- to 4.5-fold times the native TEF promoter. Further analysis through transcription factor binding site abrogation revealed the GCR1p binding site to be necessary for complete UASTEF#2 function. These various promoters were tested for function in a variety of carbon sources. Finally, by combining disparate UAS elements (in this case, UASTEF and UAS1B), we developed a high-strength promoter with for Y. lipolytica with an expression level of nearly sevenfold higher than that of the strong, constitutive TEF promoter. Thus, the general strategy described here enables the efficient, de novo construction of synthetic promoters to both increase native expression capacity and to produce libraries for tunable gene expression.

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters.

A dynamic range of well-controlled constitutive and tunable promoters are essential for metabolic engineering and synthetic biology applications in all host organisms. Here, we apply a synthetic hybrid promoter approach for the creation of strong promoter libraries in the model yeast, Saccharomyces cerevisiae. Synthetic hybrid promoters are composed of two modular components-the enhancer element, consisting of tandem repeats or combinations of upstream activation sequences (UAS), and the core promoter element. We demonstrate the utility of this approach with three main case studies. First, we establish a dynamic range of constitutive promoters and in doing so expand transcriptional capacity of the strongest constitutive yeast promoter, P(GPD) , by 2.5-fold in terms of mRNA levels. Second, we demonstrate the capacity to impart synthetic regulation through a hybrid promoter approach by adding galactose activation and removing glucose repression. Third, we establish a collection of galactose-inducible hybrid promoters that span a nearly 50-fold dynamic range of galactose-induced expression levels and increase the transcriptional capacity of the Gal1 promoter by 15%. These results demonstrate that promoters in S. cerevisiae, and potentially all yeast, are enhancer limited and a synthetic hybrid promoter approach can expand, enhance, and control promoter activity.

Clinician and patient beliefs about diagnostic imaging for low back pain: a systematic qualitative evidence synthesis.

OBJECTIVE: Overuse of diagnostic imaging for patients with low back pain remains common. The underlying beliefs about diagnostic imaging that could drive overuse remain unclear. We synthesised qualitative research that has explored clinician, patient or general public beliefs about diagnostic imaging for low back pain. DESIGN: A qualitative evidence synthesis using a thematic analysis. METHODS: We searched MEDLINE, EMBASE, CINAHL, AMED and PsycINFO from inception to 17 June 2019. Qualitative studies that interviewed clinicians, patients and/or general public exploring beliefs about diagnostic imaging for low back pain were included. Four review authors independently extracted data and organised these according to themes and subthemes. We used the Critical Appraisal Skills Programme tool to critically appraise included studies. To assess confidence in review findings, we used the GRADE-Confidence in the Evidence from Reviews of Qualitative Research method. RESULTS: We included 69 qualitative studies with 1747 participants. Key findings included: Patients and clinicians believe diagnostic imaging is an important test to locate the source of low back pain (33 studies, high confidence); patients with chronic low back pain believe pathological findings on diagnostic imaging provide evidence that pain is real (12 studies, moderate confidence); and clinicians ordered diagnostic imaging to reduce the risk of a missed diagnosis that could lead to litigation, and to manage patients' expectations (12 studies, moderate confidence). CONCLUSION: Clinicians and patients can believe that diagnostic imaging is an important tool for locating the source of non-specific low back pain. Patients may underestimate the harms of unnecessary imaging tests. These beliefs could be important targets for intervention. PROSPERO REGISTRATION NUMBER: CRD42017076047.

An in vitro diagnostic certified point of care single nucleotide test for IL28B polymorphisms.

Numerous genetic polymorphisms have been identified as associated with disease or treatment outcome, but the routine implementation of genotyping into actionable medical care remains limited. Point-of-care (PoC) technologies enable rapid and real-time treatment decisions, with great potential for extending molecular diagnostic approaches to settings with limited medical infrastructure (e.g., CLIA certified diagnostic laboratories). With respect to resource-limited settings, there is a need for simple devices to implement biomarker guided treatment strategies. One relevant example is chronic hepatitis C infection, for which several treatment options are now approved. Single nucleotide polymorphisms (SNPs) in the IL-28B / IFNL3 locus have been well described to predict both spontaneous clearance and response to interferon based therapies. We utilized the Genedrive® platform to develop an assay for the SNP rs12979860 variants (CC, CT and TT). The assay utilizes a hybrid thermal engine, permitting rapid heating and cooling, enabling an amplification based assay with genetic variants reported using endpoint differential melting cure analysis in less than 60 minutes. We validated this assay using non-invasive buccal swab sampling in a prospective study of 246 chronic HCV patients, achieving 100% sensitivity and 100% specificity (95% exact CI: 98.8-100%)) in 50 minutes as compared to conventional lab based PCR testing. Our results provide proof of concept that precision medicine is feasible in resource-limited settings, offering the first CE-IVD (in vitro diagnostics) validated PoC SNP test. We propose that IL-28B genotyping may be useful for directing patients towards lower cost therapies, and rationing use of costly direct antivirals for use in those individuals showing genetic risk.

Biotechnological applications of bacterial protein secretion: from therapeutics to biofuel production.

Recent years have witnessed significant progresses in engineering of recombinant protein secretion. The relatively simple secretion mechanisms, Type I and Type V (autotransporters), are increasingly used for secretion of recombinant proteins. The secretion level of target proteins varied from milligrams to grams per liter. The range of proteins was significantly expanded beyond medical application. Notable additions include biofuel productions from renewable feedstock. Despite the progress, almost all successes in the engineering efforts come with significant trials and errors, highlighting the need for a better understanding of secretion systems and rational based methods.

Evolution of an alkane-inducible biosensor for increased responsiveness to short-chain alkanes.

Synthetic alkane-inducible biosensors have applications as detectors for environmental hydrocarbon contamination and as novel inducible expression systems with low-cost inducers. Here, we have assembled and evolved an alkane-responsive biosensor with a fluorescence output signal in Escherichia coli by utilizing regulatory machinery from Pseudomonas putida's alkane metabolism. Within our system, the transcriptional regulator, AlkSp, is activated by the presence of alkanes and binds to the P(alkB) promoter, stimulating transcription of a Green Fluorescent Protein reporter. Through two successive rounds of directed evolution via error prone PCR and fluorescence activated cell sorting, we isolated alkS mutants enabling up to a 5 fold increase in fluorescence output signal in response to short-chain alkanes such as hexane and pentane. Further characterization of selected mutants demonstrated altered responsiveness to a wide range of linear alkanes (pentane to dodecane). Sequence analysis highlighted the S470T mutation as a likely candidate responsible for increased effectiveness of the AlkS protein for short-chain alkanes. This work represents the first evolution of a synthetic biosensor system for alkanes.

Aminopeptidase N (CD13) regulates tumor necrosis factor-alpha-induced apoptosis in human neutrophils.

Neutrophil apoptosis plays a central role in the resolution of granulocytic inflammation. We have shown previously that tumor necrosis factor-alpha (TNFalpha) enhances the rate of neutrophil apoptosis at early time points via a mechanism involving both TNF receptor (TNFR) I and TNFRII. Here we reveal a marked but consistent variation in the magnitude of the pro-apoptotic effect of TNFalpha in neutrophils isolated from healthy donors, and we show that inhibition of cell surface aminopeptidase N (APN) using actinonin, bestatin, or inhibitory peptides significantly enhanced the efficacy of TNFalpha-induced killing. Notably, an inverse correlation is shown to exist between neutrophil APN activity and the sensitivity of donor cells to TNFalpha-induced apoptosis. Inhibition of cell surface APN appears to interfere with the shedding of TNFRI, and as a consequence results in augmented TNFalpha-induced apoptosis, cell polarization, and TNFalpha-primed, formyl-methionyl-leucyl-phenylalanine-stimulated respiratory burst. Of note, actinonin and bestatin had no effect on TNFRII expression under resting or TNFalpha-stimulated conditions and did not alter CXCRI or CXCRII expression. These data suggest significant variation in the activity of APN/CD13 on the cell surface of neutrophils in normal individuals and reveal a novel mechanism whereby APN/CD13 regulates TNFalpha-induced apoptosis via inhibition of TNFRI shedding. This has therapeutic relevance for driving neutrophil apoptosis in vivo.