Design principles for riboswitch function

Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the construction of tunable regulatory components based on its rich regulatory capacity and our current understanding of the sequence–function relationship. One prominent example of RNA-based regulatory components is riboswitches, genetic elements that mediate ligand control of gene expression through diverse regulatory mechanisms. While characterization of natural and synthetic riboswitches has revealed that riboswitch function can be modulated through sequence alteration, no quantitative frameworks exist to investigate or guide riboswitch tuning. Here, we combined mathematical modeling and experimental approaches to investigate the relationship between riboswitch function and performance. Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms. We also found that practical system restrictions, such as an upper limit on ligand concentration, can significantly alter the requirements for riboswitch performance, necessitating alternative tuning strategies. Previous experimental data for natural and synthetic riboswitches as well as experiments conducted in this work support model predictions. From our results, we developed a set of general design principles for synthetic riboswitches. Our results also provide a foundation from which to investigate how natural riboswitches are tuned to meet systems-level regulatory demands

Human saliva and model saliva at bulk to adsorbed phases – similarities and differences

Human saliva, a seemingly simple aqueous fluid, is, in fact, an extraordinarily complex biocolloid that is not fully understood, despite many decades of study. Salivary lubrication is widely believed to be a signature of good oral health and is also crucial for speech, food oral processing and swallowing. However, saliva has been often neglected in food colloid research, primarily due to its high intra- to inter-individual variability and altering material properties upon collection and storage, when used as an ex vivo research material. In the last decade, colloid scientists have attempted designing model (i.e. ‘saliva mimicking fluid’) saliva formulations to understand saliva-food colloid interactions in an in vitro set up and its contribution on microstructural aspects, lubrication properties and sensory perception. In this Review, we critically examine the current state of knowledge on bulk and interfacial properties of model saliva in comparison to real human saliva and highlight how far such model salivary formulations can match the properties of real human saliva. Many, if not most, of these model saliva formulations share similarities with real human saliva in terms of biochemical compositions, including electrolytes, pH and concentrations of salivary proteins, such as α-amylase and highly glycosylated mucins. This, together with similarities between model and real saliva in terms of surface charge, has led to significant advancement in decoding colloidal interactions (bridging, depletion) of charged emulsion droplets and associated sensory perception in the oral phase. However, model saliva represents significant dissimilarity to real saliva in the lubricating properties. Based on in-depth examination of properties of mucins from animal sources (e.g. pig gastric mucins (PGM) or bovine submaxillary mucin (BSM)), we can recommend that BSM is currently the most optimal mucin source when attempting to replicate saliva based on surface adsorption and lubrication properties. Even though purification via dialysis or chromatographic techniques may influence various physicochemical properties of BSM, such as structure and surface adsorption, the lubricating properties of model saliva formulations based on BSM are generally superior and more reliable than PGM counterpart at orally relevant pH. Comparison of mucin-containing model saliva with ex vivo human salivary conditioning films suggests that mucin alone cannot replicate the lubricity of real human salivary pellicle. Mucin-based multi-layers containing mucin and oppositely charged polyelectrolytes may offer promising avenues in the future for engineering biomimetic salivary pellicle, however, this has not been explored in oral tribology experiments to date. Hence, there is a strong need for systematic studies with employment of model saliva formulations containing mucins with and without polycationic additives before a consensus on a standardized model saliva formulation can be achieved. Overall, this review provides a comprehensive framework on simulating saliva for a particular bulk or surface property when doing food oral processing experiments

Controversy and consensus on indications for sperm DNA fragmentation testing in male infertility: a global survey, current guidelines, and expert recommendations.

PURPOSE: Sperm DNA fragmentation (SDF) testing was recently added to the sixth edition of the World Health Organization laboratory manual for the examination and processing of human semen. Many conditions and risk factors have been associated with elevated SDF; therefore, it is important to identify the population of infertile men who might benefit from this test. The purpose of this study was to investigate global practices related to indications for SDF testing, compare the relevant professional society guideline recommendations, and provide expert recommendations. MATERIALS AND METHODS: Clinicians managing male infertility were invited to take part in a global online survey on SDF clinical practices. This was conducted following the CHERRIES checklist criteria. The responses were compared to professional society guideline recommendations related to SDF and the appropriate available evidence. Expert recommendations on indications for SDF testing were then formulated, and the Delphi method was used to reach consensus. RESULTS: The survey was completed by 436 experts from 55 countries. Almost 75% of respondents test for SDF in all or some men with unexplained or idiopathic infertility, 39% order it routinely in the work-up of recurrent pregnancy loss (RPL), and 62.2% investigate SDF in smokers. While 47% of reproductive urologists test SDF to support the decision for varicocele repair surgery when conventional semen parameters are normal, significantly fewer general urologists (23%; p=0.008) do the same. Nearly 70% would assess SDF before assisted reproductive technologies (ART), either always or for certain conditions. Recurrent ART failure is a common indication for SDF testing. Very few society recommendations were found regarding SDF testing. CONCLUSIONS: This article presents the largest global survey on the indications for SDF testing in infertile men, and demonstrates diverse practices. Furthermore, it highlights the paucity of professional society guideline recommendations. Expert recommendations are proposed to help guide clinicians

Characterization of Proliferating Lesion-Resident Cells During All Stages of Atherosclerotic Growth.

BACKGROUND: Monocyte recruitment leads to accumulation of macrophage foam cells and contributes to atherosclerotic lesion growth. Recent studies have reported that lesion-resident macrophages can proliferate and represent a major cellular component during lesion development. This study was designed to assess whether the rate of macrophage proliferation changes during well-established stages of lesion growth and to characterize other populations of proliferating cells within these lesions. METHODS AND RESULTS: Using murine models of atherosclerosis (Apoe(-/-) and LDLr(-/-) mice) and human coronary artery lesions, in situ proliferation of lesion-resident cells at different stages of growth was assessed by staining for Ki67 and bromodeoxyuridine (BrdU). In early lesions, close to half of all actively growing macrophages were proliferating in situ. BrdU pulse labeling allowed for accurate identification of in situ proliferating macrophages compared to those derived from monocyte recruitment. Local macrophage proliferation declined as lesions advanced. Interestingly, intimal inflammatory cell infiltrates containing proliferating T lymphocytes were identified during the active phase of lesion growth and correlated with apoptotic cell death. Inflammatory cell infiltrates were completely resolved in advanced lesions and replaced with the necrotic core. CONCLUSIONS: Our findings indicate that atherosclerotic lesions contain locally proliferating macrophages primarily during early and intermediate stages of lesion growth. Furthermore, T-lymphocyte-enriched inflammatory cell infiltrates represent a novel subset of proliferating cells within the atherosclerotic lesion that correlate with apoptosis and precede the necrotic core. These findings have novel implications in understanding the pathogenesis of atherosclerosis and may implicate proliferating T lymphocytes as a contributing factor to lesion progression and stability

Indolo-naphthyridine-6,13-dione thiophene building block for conjugated polymer electronics: Molecular origin of ultrahigh n-type mobility

Herein, we present the synthesis and characterization of four conjugated polymers containing a novel chromophore for organic electronics based on an indigoid structure. These polymers exhibit extremely small band gaps of ∼1.2 eV, impressive crystallinity, and extremely high n-type mobility exceeding 3 cm2 V s–1. The n-type charge carrier mobility can be correlated with the remarkably high crystallinity along the polymer backbone having a correlation length in excess of 20 nm. Theoretical analysis reveals that the novel polymers have highly rigid nonplanar geometries demonstrating that backbone planarity is not a prerequisite for either narrow band gap materials or ultrahigh mobilities. Furthermore, the variation in backbone crystallinity is dependent on the choice of comonomer. OPV device efficiencies up to 4.1% and charge photogeneration up to 1000 nm are demonstrated, highlighting the potential of this novel chromophore class in high-performance organic electronics

Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering