Role of riboswitches in gene regulation and their potential for algal biotechnology.

Riboswitches are regulatory elements in messenger RNA to which specific ligands can bind directly in the absence of proteins. Ligand binding alters the mRNA secondary structure, thereby affecting expression of the encoded protein. Riboswitches are widespread in prokaryotes, with over 20 different effector ligands known, including amino acids, cofactors, and Mg(2+) ions, and gene expression is generally regulated by affecting translation or termination of transcription. In plants, fungi, and microalgae, riboswitches have been found, but only those that bind thiamine pyrophosphate. These eukaryotic riboswitches operate by causing alternative splicing of the transcript. Here, we review the current status of riboswitch research with specific emphasis on microalgae. We discuss new riboswitch discoveries and insights into the underlying mechanism of action, and how next generation sequencing technology provides the motivation and opportunity to improve our understanding of these rare but important regulatory elements. We also highlight the potential of microalgal riboswitches as a tool for synthetic biology and industrial biotechnology.G.T.D.T.N was funded in part by Murray Edwards College and the Cambridge Philosophical Society. M.A.S was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/I00680X/1 and the European Commission 7th Framework Programme (FP7) project SPLASH (Sustainable PoLymers from Algae Sugars and Hydrocarbons), grant agreement number 311956. K.E.H was funded by BBSRC grant BB/I013164/1.This is the author accepted manuscript. The final version is available from Wiley via https://doi.org/10.1111/jpy.1241

Establishing Chlamydomonas reinhardtii as an industrial biotechnology host.

Microalgae constitute a diverse group of eukaryotic unicellular organisms that are of interest for pure and applied research. Owing to their natural synthesis of value-added natural products microalgae are emerging as a source of sustainable chemical compounds, proteins and metabolites, including but not limited to those that could replace compounds currently made from fossil fuels. For the model microalga, Chlamydomonas reinhardtii, this has prompted a period of rapid development so that this organism is poised for exploitation as an industrial biotechnology platform. The question now is how best to achieve this? Highly advanced industrial biotechnology systems using bacteria and yeasts were established in a classical metabolic engineering manner over several decades. However, the advent of advanced molecular tools and the rise of synthetic biology provide an opportunity to expedite the development of C. reinhardtii as an industrial biotechnology platform, avoiding the process of incremental improvement. In this review we describe the current status of genetic manipulation of C. reinhardtii for metabolic engineering. We then introduce several concepts that underpin synthetic biology, and show how generic parts are identified and used in a standard manner to achieve predictable outputs. Based on this we suggest that the development of C. reinhardtii as an industrial biotechnology platform can be achieved more efficiently through adoption of a synthetic biology approach.M.A.S and J.R were funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/I00680X/1, M.A.S was also funded by the European Commission 7th Framework Programme (FP7) project SPLASH (Sustainable PoLymers from Algae Sugars and Hydrocarbons), grant agreement number 311956. G.T.D.T.N was funded in part by Murray Edwards College and the Cambridge Philosophical Society. D.L. was funded by the Bill and Melinda Gates Foundation, and K.E.H was funded by BBSRC grant BB/I013164/1.This paper was originally published in The Plant Journal (Scaife MA, Nguyen GTDT, Rico J, Lambert D, Helliwell KE, Smith AG, The Plant Journal 2015, doi:10.1111/tpj.12781)

Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways

Synovial fibroblasts in persistent inflammatory arthritis have been suggested to have parallels with cancer growth and wound healing, both of which involve a stereotypical serum response programme. We tested the hypothesis that a serum response programme can be used to classify diseased tissues, and investigated the serum response programme in fibroblasts from multiple anatomical sites and two diseases. To test our hypothesis we utilized a bioinformatics approach to explore a publicly available microarray dataset including rheumatoid arthritis (RA), osteoarthritis (OA) and normal synovial tissue, then extended those findings in a new microarray dataset representing matched synovial, bone marrow and skin fibroblasts cultured from RA and OA patients undergoing arthroplasty. The classical fibroblast serum response programme discretely classified RA, OA and normal synovial tissues. Analysis of low and high serum treated fibroblast microarray data revealed a hierarchy of control, with anatomical site the most powerful classifier followed by response to serum and then disease. In contrast to skin and bone marrow fibroblasts, exposure of synovial fibroblasts to serum led to convergence of RA and OA expression profiles. Pathway analysis revealed three inter-linked gene networks characterising OA synovial fibroblasts: Cell remodelling through insulin-like growth factors, differentiation and angiogenesis through -3 integrin, and regulation of apoptosis through CD44. We have demonstrated that Fibroblast serum response signatures define disease at the tissue level, and that an OA specific, serum dependent repression of genes involved in cell adhesion, extracellular matrix remodelling and apoptosis is a critical discriminator between cultured OA and RA synovial fibroblasts

Contribution of bone turnover markers to the variation in bone mineral density: a study in Vietnamese men and women

© 2018, International Osteoporosis Foundation and National Osteoporosis Foundation. Summary: The present cross-sectional study constructed reference ranges for bone resorption marker beta isomerized form of C-terminal crosslinking telopeptides of type I collagen (beta-CTX) and bone formation marker procollagen type 1 N-terminal propeptide (PINP) for the Vietnamese population. We have further shown that for a given age and weight, higher levels of beta-CTX were significantly associated with bone mineral density in men and women. Introduction: Normal bone is constantly renewed by two opposing processes of resorption and formation which can be reflected by bone turnover markers (BTMs). This study sought to define the contribution of BTMs to the variation in bone mineral density (BMD) in normal individuals. Methods: The study involved 205 men and 432 women aged between 18 and 87, who were randomly selected from various districts within Ho Chi Minh City, Vietnam. Fasting serum levels of PINP and beta-CTX were determined by electrochemiluminescence (Roche, ECLIA). BMD at the lumbar spine (LS) and femoral neck (FN) was measured by dual-energy x-ray absorptiometry (Hologic, Waltham, MA, USA). Results: Among those aged 50 years, women had higher PINP and beta-CTX levels than men. In the multiple linear regression analysis, beta-CTX—but not PINP—was significantly associated with both femoral neck (P = 0.008) and lumbar spine BMD (P = 0.008) and the association was independent of gender, age, and body weight. The proportion of variance in BMD attributable to beta-CTX was 1% for femoral neck BMD and 2% for lumbar spine BMD. Conclusion: The elevation in bone formation marker PINP and bone resorption marker beta-CTX in postmenopausal women was greater than in elderly men. However, only beta-CTX was modestly but significantly associated with BMD

Feasibility of establishing a rehabilitation programme in a Vietnamese intensive care unit

Increasing numbers of people are surviving critical illness throughout the world, but survivorship is associated with long-term disability. In high-income settings physical rehabilitation is commonly employed to counter this and improve outcomes. These utilize highly-trained multidisciplinary teams and are unavailable and unaffordable in most low and middle income countries (LMICs). We aimed to design a sustainable intensive care unit (ICU) rehabilitation program and to evaluate its feasibility in a LMIC setting. In this project patients, care-givers and experts co-designed an innovative rehabilitation programme that can be delivered by non-expert ICU staff and family care-givers in a LMIC. We implemented this programme in adult patient with patients with tetanus at the Hospital for Tropical Diseases, Ho Chi Minh City over a 5-month period, evaluating the programme's acceptability, enablers and barriers. A 6-phase programme was designed, supported by written and video material. The programme was piloted in total of 30 patients. Rehabilitation was commenced a median 14 (inter quartile range (IQR) 10-18) days after admission. Each patient received a median of 25.5 (IQR 22.8-34.8) rehabilitation sessions out of a median 27 (22.8-35) intended (prescribed) sessions. There were no associated adverse events. Patients and staff found rehabilitation to be beneficial, enhanced relationships between carers, patients and staff and was deemed to be a positive step towards recovery and return to work. The main barrier was staff time. The programme was feasible for patients with tetanus and viewed positively by staff and participants. Staff time was identified as the major barrier to ongoing implementation

Endothelial Nitric Oxide Pathways in the Pathophysiology of Dengue: A Prospective Observational Study

Background: Dengue can cause increased vascular permeability that may lead to hypovolemic shock. Endothelial dysfunction may underlie this; however, the association of endothelial nitric oxide (NO) pathways with disease severity is unknown. Methods: We performed a prospective observational study in 2 Vietnamese hospitals, assessing patients presenting early (<72 hours of fever) and patients hospitalized with warning signs or severe dengue. The reactive hyperemic index (RHI), which measures endothelium-dependent vasodilation and is a surrogate marker of endothelial function and NO bioavailability, was evaluated using peripheral artery tonometry (EndoPAT), and plasma levels of l-arginine, arginase-1, and asymmetric dimethylarginine were measured at serial time-points. The main outcome of interest was plasma leakage severity. Results: Three hundred fourteen patients were enrolled; median age of the participants was 21(interquartile range, 13-30) years. No difference was found in the endothelial parameters between dengue and other febrile illness. Considering dengue patients, the RHI was significantly lower for patients with severe plasma leakage compared to those with no leakage (1.46 vs 2.00; P < .001), over acute time-points, apparent already in the early febrile phase (1.29 vs 1.75; P = .012). RHI correlated negatively with arginase-1 and positively with l-arginine (P = .001). Conclusions: Endothelial dysfunction/NO bioavailability is associated with worse plasma leakage, occurs early in dengue illness and correlates with hypoargininemia and high arginase-1 levels