Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.

Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a "Chicken and Egg" problem; its resolution is concisely described by de Grasse Tyson: "The egg was laid by a bird that was not a chicken". The concision and generality of that answer furnish no details-only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. In each example, a paradox is resolved by coupling "if, and only if" conditions for reciprocal transitions between levels, such that the consequent of the first test is the antecedent for the second. Each condition thus restricts fluxes through, or "gates" the other. Reciprocally-coupled gating, in which two gated processes constrain one another, is self-referential, hence maps onto the formal structure of "strange loops". That mapping uncovers two different kinds of forces that may help unite the axioms underlying three phenomena that distinguish biology from chemistry. As a physical analog for Gödel's logic, biomolecular strange-loops provide a natural metaphor around which to organize a large body of experimental data, linking biology to information, free energy, and the second law of thermodynamics.

Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.

We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, Iσ; an impedance parameter, Z; and an effective alphabet size, neff; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small.

Agonist bias and agonist-dependent antagonism at corticotrophin releasing factor receptors.

The corticotropin-releasing factor (CRF) receptors represent potential drug targets for the treatment of anxiety, stress, and other disorders. However, it is not known if endogenous CRF receptor agonists display biased signaling, how effective CRF receptor antagonists are at blocking different agonists and signaling pathways or how receptor activity-modifying proteins (RAMPs) effect these processes. This study aimed to address this by investigating agonist and antagonist action at CRF1 and CRF2 receptors. We used CRF1 and CRF2 receptor transfected Cos7 cells to assess the ability of CRF and urocortin (UCN) peptides to activate cAMP, inositol monophosphate (IP1 ), and extracellular signal-regulated kinase 1/2 signaling and determined the ability of antagonists to block agonist-stimulated cAMP and IP1 accumulation. The ability of RAMPs to interact with CRF receptors was also examined. At the CRF1 receptor, CRF and UCN1 activated signaling in the same manner. However, at the CRF2 receptor, UCN1 and UCN2 displayed similar signaling profiles, whereas CRF and UCN3 displayed bias away from IP1 accumulation over cAMP. The antagonist potency was dependent on the receptor, agonist, and signaling pathway. CRF1 and CRF2 receptors had no effect on RAMP1 or RAMP2 surface expression. The presence of biased agonism and agonist-dependent antagonism at the CRF receptors offers new avenues for developing drugs tailored to activate a specific signaling pathway or block a specific agonist. Our findings suggest that the already complex CRF receptor pharmacology may be underappreciated and requires further investigation.

Experimental solutions to problems defining the origin of codon-directed protein synthesis.

How genetic coding differentiated biology from chemistry is a long-standing challenge in Biology, for which there have been few experimental approaches, despite a wide-ranging speculative literature. We summarize five coordinated areas-experimental characterization of functional approximations to the minimal peptides (protozymes and urzymes) necessary to activate amino acids and acylate tRNA; showing that specificities of these experimental models match those expected from the synthetase Class division; population of disjoint regions of amino acid sequence space via bidirectional coding ancestry of the two synthetase Classes; showing that the phase transfer equilibria of amino acid side chains that form a two-dimensional basis set for protein folding are embedded in patterns of bases in the tRNA acceptor stem and anticodon; and identification of molecular signatures of ancestral synthetases and tRNAs necessary to define the earliest cognate synthetase:tRNA pairs-that now compose an extensive experimentally testable paradigm for progress toward understanding the coordinated emergence of the codon table and viable mRNA coding sequences. We briefly discuss recent progress toward identifying the remaining outstanding questions-the nature of the earliest amino acid alphabets and the origin of binding discrimination via distinct amino acid sequence-independent protein secondary structures-and how these, too, might be addressed experimentally.

Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding.

Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. The resulting inversion symmetries in aaRS structural biology would have stabilized the initial and subsequent differentiation of coding specificities, rapidly promoting diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexive, nanoenvironmental sensing in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: 1) aaRS enzymes must be interdependent; 2) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; 3) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; and 4) the Central Dogma's emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene-replicase-translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today.

The effectiveness of a group cognitive-behavioural breathlessness intervention on health status, mood and hospital admissions in elderly patients with chronic obstructive pulmonary disease.

Non-pharmacological breathlessness interventions in lung cancer have proven beneficial. Breathlessness is also a major symptom in chronic obstructive pulmonary disease (COPD). This study measured the effectiveness of a non-exercise-based four-week cognitive-behavioural breathlessness intervention, delivered in a group setting for elderly patients with severe COPD. The results of the one-year feasibility study are presented. Patients with COPD were asked to complete the St. George's Respiratory Questionnaire and Hospital Anxiety and Depression Scale six weeks before the intervention, at the start and end of the intervention and at six weeks follow-up. The multidisciplinary intervention used a cognitive-behavioural format to address understanding of COPD and medication, anxiety, panic and depression, activity pacing, relaxation, breathing retraining and goal-setting. Retrospective data on accident & emergency (A&E) attendances and length of hospital stay was collected six months before and six months after the intervention and the data compared to a matched waiting list control group. The results showed significant improvements in depression and health status. There was a non-significant improvement in anxiety. There was a significant reduction in A&E attendance and a non-significant reduction in length of hospital stay in the intervention group, compared to comparative increases in the control group, highlighting the cost-effectiveness of the intervention.

Inhaled mannitol in cystic fibrosis.

Inhaled mannitol has recently been given fast-track status as an investigational drug to treat the lung manifestations of cystic fibrosis. It seems to work in a similar way to nebulized hypertonic saline, osmotically inducing water flux into the bronchial lumen, thereby increasing the hydration of airway mucus, which can then be cleared more effectively by mucociliary clearance and coughing. Short-term studies have shown good tolerability and improvements in lung mucociliary clearance. Longer-term studies studying end points of clinical relevance are ongoing. This article assesses its likely future role in cystic fibrosis.

Effect of osmolality on mucociliary transportability and rheology of cystic fibrosis and bronchiectasis sputum.

OBJECTIVE: Water is the main constituent of mucus, and its concentration is likely to be important in all aspects of mucus function, including ciliary clearance. The objective of this study was to investigate the effect of water content and osmolality of the mucus on mucociliary transportability. METHODOLOGY: Rheology and ciliary transportability of 10 sputum samples that had been subjected to various manipulations were measured using a mucus-depleted bovine trachea model. RESULTS: It was shown that addition of sodium chloride 0.2 Osmoles/kg (0.585% weight for weight) increased the transportability by 41% (P < 0.01). Evaporation of the sputum to 50% of its original weight caused a 118% increase in transportability (P < 0.0006), but iso-osmolal removal of 50% of the liquid with filter cards led to a non-significant, 25% increase in transportability. Parallel plate viscoelasticity was approximately doubled in both the evaporated and liquid-depleted samples, but was not changed by the addition of 0.2 Osmoles/kg of sodium chloride. The correlation between the osmolality of sputum and ciliary transportability (r = 0.54, P= 0.005) was better than the correlations between the viscosity (r = 0.21, P= 0.27) or elasticity (r = 0.23, P= 0.23) and ciliary transportability. CONCLUSIONS: These results suggest that the osmolality of sputum exerts a greater influence on mucociliary clearance than its viscoelastic properties.