Hierarchical biomechanics: student engagement activities with a focus on biological physics

Hierarchical structure and mechanics are crucial in biological systems as they allow for smaller molecules, such as proteins and sugars, to be used in the construction of large scale biological structures exhibiting properties such as structural support functionality. By exploring the fundamental principles of structure and mechanics at the macroscale, this general theme provides a clear insight into how physics can be applied to the complex questions of biology. With a focus on biopolymer networks and hydrogels, we present a series of interactive activities which cover a range of biophysical concepts at an introductory level, such as viscoelasticity, biological networks and ultimately, hierarchical biomechanics. These activities enable us to discuss multidisciplinary science with a general audience and, given the current trends of research science, this conceptualisation of science is vital for the next generation of scientists

Modelling the viral dynamics of the SARS-CoV-2 Delta and Omicron variants in different cell types.

We use viral kinetic models fitted to viral load data from in vitro studies to explain why the SARS-CoV-2 Omicron variant replicates faster than the Delta variant in nasal cells, but slower than Delta in lung cells, which could explain Omicron's higher transmission potential and lower severity. We find that in both nasal and lung cells, viral infectivity is higher for Omicron but the virus production rate is higher for Delta, with an estimated approximately 200-fold increase in infectivity and 100-fold decrease in virus production when comparing Omicron with Delta in nasal cells. However, the differences are unequal between cell types, and ultimately lead to the basic reproduction number and growth rate being higher for Omicron in nasal cells, and higher for Delta in lung cells. In nasal cells, Omicron alone can enter via a TMPRSS2-independent pathway, but it is primarily increased efficiency of TMPRSS2-dependent entry which accounts for Omicron's increased activity. This work paves the way for using within-host mathematical models to understand the transmission potential and severity of future variants

Reduced exercise capacity in patients with systemic sclerosis is associated with lower peak tissue oxygen extraction: a cardiovascular magnetic resonance-augmented cardiopulmonary exercise study

Background: Exercise intolerance in systemic sclerosis (SSc) is typically attributed to cardiopulmonary limitations. However, problems with skeletal muscle oxygen extraction have not been fully investigated. This study used cardiovascular magnetic resonance (CMR)-augmented cardiopulmonary exercise testing (CMR-CPET) to simultaneously measure oxygen consumption and cardiac output. This allowed calculation of arteriovenous oxygen content gradient, a recognized marker of oxygen extraction. We performed CMR-CPET in 4 groups: systemic sclerosis (SSc); systemic sclerosis-associated pulmonary arterial hypertension (SSc-PAH); non-connective tissue disease pulmonary hypertension (NC-PAH); and healthy controls. Methods: We performed CMR-CPET in 60 subjects (15 in each group) using a supine ergometer following a ramped exercise protocol until exhaustion. Values for oxygen consumption, cardiac output and oxygen content gradient, as well as ventricular volumes, were obtained at rest and peak-exercise for all subjects. In addition, T1 and T2 maps were acquired at rest, and the most recent clinical measures (hemoglobin, lung function, 6-min walk, cardiac and catheterization) were collected. Results: All patient groups had reduced peak oxygen consumption compared to healthy controls (p<0.022). The SSc and SSc-PAH groups had reduced peak oxygen content gradient compared to healthy controls (p<0.03). Conversely, the SSc-PAH and NC-PH patients had reduced peak cardiac output compared to healthy controls and SSc patients (p<0.006). Higher hemoglobin was associated with higher peak oxygen content gradient (p=0.025) and higher myocardial T1 was associated with lower peak stroke volume (p=0.011). Conclusions: Reduced peak oxygen consumption in SSc patients is predominantly driven by reduced oxygen content gradient and in SSc-PAH patients this was amplifed by reduced peak cardiac output

Ages for exoplanet host stars

Age is an important characteristic of a planetary system, but also one that is difficult to determine. Assuming that the host star and the planets are formed at the same time, the challenge is to determine the stellar age. Asteroseismology provides precise age determination, but in many cases the required detailed pulsation observations are not available. Here we concentrate on other techniques, which may have broader applicability but also serious limitations. Further development of this area requires improvements in our understanding of the evolution of stars and their age-dependent characteristics, combined with observations that allow reliable calibration of the various techniques.Comment: To appear in "Handbook of Exoplanets", eds. Deeg, H.J. & Belmonte, J.A, Springer (2018

Ethanol reversal of tolerance to the respiratory depressant effects of morphine

Opioids are the most common drugs associated with unintentional drug overdose. Death results from respiratory depression. Prolonged use of opioids results in the development of tolerance but the degree of tolerance is thought to vary between different effects of the drugs. Many opioid addicts regularly consume alcohol (ethanol), and post-mortem analyses of opioid overdose deaths have revealed an inverse correlation between blood morphine and ethanol levels. In the present study, we determined whether ethanol reduced tolerance to the respiratory depressant effects of opioids. Mice were treated with opioids (morphine, methadone, or buprenorphine) for up to 6 days. Respiration was measured in freely moving animals breathing 5% CO(2) in air in plethysmograph chambers. Antinociception (analgesia) was measured as the latency to remove the tail from a thermal stimulus. Opioid tolerance was assessed by measuring the response to a challenge dose of morphine (10 mg/kg i.p.). Tolerance developed to the respiratory depressant effect of morphine but at a slower rate than tolerance to its antinociceptive effect. A low dose of ethanol (0.3 mg/kg) alone did not depress respiration but in prolonged morphine-treated animals respiratory depression was observed when ethanol was co-administered with the morphine challenge. Ethanol did not alter the brain levels of morphine. In contrast, in methadone- or buprenorphine-treated animals no respiratory depression was observed when ethanol was co-administered along with the morphine challenge. As heroin is converted to morphine in man, selective reversal of morphine tolerance by ethanol may be a contributory factor in heroin overdose deaths

News from Lattice QCD on Heavy Quark Potentials and Spectral Functions of Heavy Quark States

We discuss recent lattice results on in-medium properties of hadrons and focus on thermal properties of heavy quark bound states. We will clarify the relation between heavy quark free energies and potentials used to analyze the melting of heavy quark bound states. Furthermore, we present calculations of meson spectral functions which indicate that the charmonium ground states, J/psi and eta_c, persist in the quark gluon plasma as well defined resonances with no significant change of their zero temperature masses at least up to T ~ 1.5 T_c. We also briefly comment on the current status of lattice calculations at non-vanishing baryon number density.Comment: Plenary talk at the 17th International Conference on Ultra Relativistic Nucleus-Nucleus Collisions (Quark Matter 2004), Oakland, California, 11-17 Jan 2004. Submitted to J.Phys.

Nucleotide supplementation: a randomised double-blind placebo controlled trial of IntestAidIB in people with Irritable Bowel Syndrome [ISRCTN67764449]

BACKGROUND: Dietary nucleotide supplementation has been shown to have important effects on the growth and development of cells which have a rapid turnover such as those in the immune system and the gastrointestinal tract. Work with infants has shown that the incidence and duration of diarrhoea is lower when nucleotide supplementation is given, and animal work shows that villi height and crypt depth in the intestine is increased as a result of dietary nucleotides. Dietary nucleotides may be semi-essential under conditions of ill-health, poor diet or stress. Since people with Irritable Bowel Syndrome tend to fulfil these conditions, we tested the hypothesis that symptoms would be improved with dietary nucleotide supplementation. METHODS: Thirty-seven people with a diagnosis of Irritable Bowel gave daily symptom severity ratings for abdominal pain, diarrhoea, urgency to have a bowel movement, incomplete feeling of evacuation after a bowel movement, bloating, flatulence and constipation for 28 days (baseline). They were then assigned to either placebo (56 days) followed by experimental (56 days) or the reverse. There was a four week washout period before crossover. During the placebo and experimental conditions participants took one 500 mg capsule three times a day; in the experimental condition the capsule contained the nutroceutical substances. Symptom severity ratings and psychological measures (anxiety, depression, illness intrusiveness and general health) were obtained and analysed by repeated measures ANOVAs. RESULTS: Symptom severity for all symptoms (except constipation) were in the expected direction of baseline>placebo>experimental condition. Symptom improvement was in the range 4 – 6%. A feeling of incomplete evacuation and abdominal pain showed the most improvement. The differences between conditions for diarrhoea, bloating and flatulence were not significant at the p < .05 level. There were no significant differences between the conditions for any of the psychological measures. CONCLUSION: Dietary nucleotide supplementation improves some of the symptoms of irritable bowel above baseline and placebo level. As expected, placebo effects were high. Apart from abdominal pain and urgency to have a bowel movement, the improvements, while consistent, are modest, and were not accompanied by improvements in any of the psychological measures. We suggest that the percentage improvement over and above the placebo effect is a physiological effect of the nucleotide supplement on the gut. The mechanisms by which these effects might improve symptoms are discussed