Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

BACKGROUND: While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria, there are two RFs with overlapping specificity, RF1 recognizes UA(A/G) and RF2 recognizes U(A/G)A. THE HYPOTHESIS: First, we hypothesize that orthologues of the E. coli K12 pseudogene prfH encode a third class-I RF that we designate RFH. Second, it is likely that RFH responds to signals other than conventional stop codons. Supporting evidence comes from the following facts: (i) A number of bacterial genomes contain prfH orthologues with no discernable interruptions in their ORFs. (ii) RFH shares strong sequence similarity with other class-I bacterial RFs. (iii) RFH contains a highly conserved GGQ motif associated with peptidyl hydrolysis activity (iv) residues located in the areas supposedly interacting with mRNA and the ribosomal decoding center are highly conserved in RFH, but different from other RFs. RFH lacks the functional, but non-essential domain 1. Yet, RFH-encoding genes are invariably accompanied by a highly conserved gene of unknown function, which is absent in genomes that lack a gene for RFH. The accompanying gene is always located upstream of the RFH gene and with the same orientation. The proximity of the 3' end of the former with the 5' end of the RFH gene makes it likely that their expression is co-regulated via translational coupling. In summary, RFH has the characteristics expected for a class-I RF, but likely with different specificity than RF1 and RF2. TESTING THE HYPOTHESIS: The most puzzling question is which signals RFH recognizes to trigger its release function. Genetic swapping of RFH mRNA recognition components with its RF1 or RF2 counterparts may reveal the nature of RFH signals. IMPLICATIONS OF THE HYPOTHESIS: The hypothesis implies a greater versatility of release-factor like activity in the ribosomal A-site than previously appreciated. A closer study of RFH may provide insight into the evolution of the genetic code and of the translational machinery responsible for termination of translation. REVIEWERS: This article was reviewed by Daniel Wilson (nominated by Eugene Koonin), Warren Tate (nominated by Eugene Koonin), Yoshikazu Nakamura (nominated by Eugene Koonin) and Eugene Koonin

Signal peptide peptidase (SPP) dimer formation as assessed by fluorescence lifetime imaging microscopy (FLIM) in intact cells

BACKGROUND: Signal peptide peptidase (SPP) is an intramembrane cleaving protease identified by its cleavage of several type II membrane signal peptides. Conservation of intramembrane active site residues demonstrates that SPP, SPP family members, and presenilins (PSs) make up a family of intramembrane cleaving proteases. Because SPP appears to function without additional protein cofactors, the study of SPP may provide structural insights into the mechanism of intramembrane proteolysis by this biomedically important family of proteins. Previous studies have shown that SPP isolated from cells appears to be a homodimer, but some evidence exists that in vitro SPP may be active as a monomer. We have conducted additional experiments to determine if SPP exists as a monomer or dimer in vivo. RESULTS: Fluorescence lifetime imaging microscopy (FLIM) can be is used to determine intra- or intermolecular interactions by fluorescently labeling epitopes on one or two different molecules. If the donor and acceptor fluorophores are less than 10 nm apart, the donor fluorophore lifetime shortens proportionally to the distance between the fluorophores. In this study, we used two types of fluorescence energy transfer (FRET) pairs; cyan fluorescent protein (CFP) with yellow fluorescent protein (YFP) or Alexa 488 with Cy3 to differentially label the NH2- or COOH-termini of SPP molecules. A cell based SPP activity assay was used to show that all tagged SPP proteins are proteolytically active. Using FLIM we were able to show that the donor fluorophore lifetime of the CFP tagged SPP construct in living cells significantly decreases when either a NH2- or COOH-terminally YFP tagged SPP construct is co-transfected, indicating close proximity between two different SPP molecules. These data were then confirmed in cell lines stably co-expressing V5- and FLAG-tagged SPP constructs. CONCLUSION: Our FLIM data strongly suggest dimer formation between two separate SPP proteins. Although the tagged SPP constructs are expressed throughout the cell, SPP dimer detection by FLIM is seen predominantly at or near the plasma membrane

Atorvastatin and vitamin e accelerates NASH resolution by dietary intervention in a preclinical guinea pig model

Despite affecting millions of patients worldwide, no pharmacological treatment has yet proved effective against non-alcoholic steatohepatitis (NASH) induced liver fibrosis. Current guidelines recommend lifestyle modifications including reductions in dietary energy intake. Recently, therapy with atorvastatin and vitamin E (vitE) has been recommended, although clinical studies on the resolution of hepatic fibrosis are inconclusive. Targeting NASH-induced hepatic end-points, this study evaluated the effects of atorvastatin and vitE alone or in combination with a dietary intervention in the guinea pig NASH model. Guinea pigs (n = 72) received 20 weeks of high fat feeding before allocating to four groups: continued HF feeding (HF), HF diet with atorvastatin and vitE (HF+), low-fat diet (LF) and low-fat with atorvastatin and vitE (LF+), for four or eight weeks of intervention. Both LF and LF+ decreased liver weight, cholesterol and plasma dyslipidemia. LF+ further improved hepatic histopathological hallmarks (p < 0.05), liver injury markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT) (p < 0.05) and reduced the expression of target genes of hepatic inflammation and fibrosis (p < 0.05), underlining an increased effect on NASH resolution in this group. Collectively, the data support an overall beneficial effect of diet change, and indicate that atorvastatin and vitE therapy combined with a diet change act synergistically in improving NASH-induced endpoints

Constructing Policy Success for UK Energy Feedback

Energy feedback tools are commonly used to promote energy saving. In the UK, energy feedback provision (currently via an In-Home Display) is part of the government-mandated roll-out of smart meters to all homes by 2020. A core assumption underlying this widespread provision is that information, or evidence, can lead to positive changes in action. This is analogous to assumptions underlying the notion of ‘Evidence-Based Policy’, which raises questions about how users, researchers and policymakers go about using evidence in aiming for a ‘successful’ outcome. In addition the ‘policy feedback’ research agenda has asked how policies alter the landscapes within which they operate by, for example, affecting relationships between actors. Via an in-depth review of DECC (now BEIS) policy literature over 2010-2016, the UK smart meter roll-out was analysed in terms of how its energy feedback focussed measures may be deemed as ‘successful’. Findings include that direct energy savings played a smaller role than might be expected, and translation from one success measure to another was repeatedly observed. A key conclusion is that acting on feedback requires an assessment of success, but such assessment is highly contextual, for consumers and policymakers alike. Ways to increase reflexivity in this area are discussed

An asymptotic model in acoustics : acoustic drift equations

A rigorous asymptotic procedure with the Mach number as a small parameter is used to derive the equations of mean flows which coexist and are affected by the background acoustic waves in the limit of very high Reynolds number

Smart homes and their users:a systematic analysis and key challenges

Published research on smart homes and their users is growing exponentially, yet a clear understanding of who these users are and how they might use smart home technologies is missing from a field being overwhelmingly pushed by technology developers. Through a systematic analysis of peer-reviewed literature on smart homes and their users, this paper takes stock of the dominant research themes and the linkages and disconnects between them. Key findings within each of nine themes are analysed, grouped into three: (1) views of the smart home-functional, instrumental, socio-technical; (2) users and the use of the smart home-prospective users, interactions and decisions, using technologies in the home; and (3) challenges for realising the smart home-hardware and software, design, domestication. These themes are integrated into an organising framework for future research that identifies the presence or absence of cross-cutting relationships between different understandings of smart homes and their users. The usefulness of the organising framework is illustrated in relation to two major concerns-privacy and control-that have been narrowly interpreted to date, precluding deeper insights and potential solutions. Future research on smart homes and their users can benefit by exploring and developing cross-cutting relationships between the research themes identified

Use of complementary and alternative medicine at Norwegian and Danish hospitals

<p>Abstract</p> <p>Background</p> <p>Several studies have found that a high proportion of the population in western countries use complementary and alternative medicine (CAM). However, little is known about whether CAM is offered in hospitals. The aim of this study was to describe to what extent CAM is offered in Norwegian and Danish hospitals and investigate possible changes in Norway since 2001.</p> <p>Methods</p> <p>A one-page questionnaire was sent to all included hospitals in both countries. The questionnaire was sent to the person responsible for the clinical activity, typically the medical director. 99 hospitals in the authority (85%) in Norway and 126 in Denmark (97%) responded. Given contact persons were interviewed.</p> <p>Results</p> <p>CAM is presently offered in about 50% of Norwegian hospitals and one-third of Danish hospitals. In Norway CAM was offered in 50 hospitals, 40 of which involved acupuncture. 19 hospitals gave other alternative therapies like biofeedback, hypnosis, cupping, ear-acupuncture, herbal medicine, art therapy, homeopathy, reflexology, thought field therapy, gestalt therapy, aromatherapy, tai chi, acupressure, yoga, pilates and other. 9 hospitals offered more than one therapy form. In Denmark 38 hospitals offered acupuncture and one Eye Movement Desensitization and Reprocessing Light Therapy. The most commonly reported reason for offering CAM was scientific evidence in Denmark. In Norway it was the interest of a hospital employee, except for acupuncture where the introduction is more often initiated by the leadership and is more based on scientific evidence of effect. All persons (except one) responsible for the alternative treatment had a medical or allied health professional background and their education/training in CAM treatment varied substantially.</p> <p>Conclusions</p> <p>The extent of CAM being offered has increased substantially in Norway during the first decade of the 21^stcentury. This might indicate a shift in attitude regarding CAM within the conventional health care system.</p

A Coin Vibrational Motor Swimming at Low Reynolds Number

Low-cost coin vibrational motors, used in haptic feedback, exhibit rotational internal motion inside a rigid case. Because the motor case motion exhibits rotational symmetry, when placed into a fluid such as glycerin, the motor does not swim even though its oscillatory motions induce steady streaming in the fluid. However, a piece of rubber foam stuck to the curved case and giving the motor neutral buoyancy also breaks the rotational symmetry allowing it to swim. We measured a 1 cm diameter coin vibrational motor swimming in glycerin at a speed of a body length in 3 seconds or at 3 mm/s. The swim speed puts the vibrational motor in a low Reynolds number regime similar to bacterial motility, but because of the oscillations of the motor it is not analogous to biological organisms. Rather the swimming vibrational motor may inspire small inexpensive robotic swimmers that are robust as they contain no external moving parts. A time dependent Stokes equation planar sheet model suggests that the swim speed depends on a steady streaming velocity V stream ~ Re 1/2s U 0 where U 0 is the velocity of surface oscillations, and streaming Reynolds number Re s = U 20/(ων) for motor angular frequency ω and fluid kinematic viscosity ν