Adaptation of gastrointestinal nematode parasites to host genotype: single locus simulation models

Background: Breeding livestock for improved resistance to disease is an increasingly important selection goal. However, the risk of pathogens adapting to livestock bred for improved disease resistance is difficult to quantify. Here, we explore the possibility of gastrointestinal worms adapting to sheep bred for low faecal worm egg count using computer simulation. Our model assumes sheep and worm genotypes interact at a single locus, such that the effect of an A allele in sheep is dependent on worm genotype, and the B allele in worms is favourable for parasitizing the A allele sheep but may increase mortality on pasture. We describe the requirements for adaptation and test if worm adaptation (1) is slowed by non-genetic features of worm infections and (2) can occur with little observable change in faecal worm egg count. Results: Adaptation in worms was found to be primarily influenced by overall worm fitness, viz. the balance between the advantage of the B allele during the parasitic stage in sheep and its disadvantage on pasture. Genetic variation at the interacting locus in worms could be from de novo or segregating mutations, but de novo mutations are rare and segregating mutations are likely constrained to have (near) neutral effects on worm fitness. Most other aspects of the worm infection we modelled did not affect the outcomes. However, the host-controlled mechanism to reduce faecal worm egg count by lowering worm fecundity reduced the selection pressure on worms to adapt compared to other mechanisms, such as increasing worm mortality. Temporal changes in worm egg count were unreliable for detecting adaptation, despite the steady environment assumed in the simulations. Conclusions: Adaptation of worms to sheep selected for low faecal worm egg count requires an allele segregating in worms that is favourable in animals with improved resistance but less favourable in other animals. Obtaining alleles with this specific property seems unlikely. With support from experimental data, we conclude that selection for low faecal worm egg count should be stable over a short time frame (e.g. 20 years). We are further exploring model outcomes with multiple loci and comparing outcomes to other control strategies

Tobacco dependence treatment for special populations: challenges and opportunities

Although smoking rates have declined in most of the countries in the world, there are population groups within these countries whose smoking rates remain significantly higher than the general population. These ‘‘forgotten groups’’ who have not been receiving the needed attention in tobacco control policies and tobacco cessation efforts include people with serious mental illness, substance use disorders, tuberculosis, people living with human immunodeficiency virus (HIV), lesbian-gaybisexual-transgender-queer people, and pregnant women. A number of steps are needed at the national level in countries where these disparities exist, including modifications to national smoking cessation treatment guidelines that address the special needs of these populations, as well as targeted smoking cessation research, since these populations are often not included in clinical trials. Because of the higher smoking prevalence in these populations, as well as their lower smoking cessation treatment success rates than the general population, more resources are needed if we are to reduce health disparities in these vulnerable populations. Additionally, we believe that more effort should be focused on integrating smoking cessation treatment in the specialized care settings frequented by these subpopulations

A protocol for ultra-high field laminar fMRI in the human brain.

Ultra-high field (UHF) neuroimaging affords the sub-millimeter resolution that allows researchers to interrogate brain computations at a finer scale than that afforded by standard fMRI techniques. Here, we present a step-by-step protocol for using UHF imaging (Siemens Terra 7T scanner) to measure activity in the human brain. We outline how to preprocess the data using a pipeline that combines tools from SPM, FreeSurfer, ITK-SNAP, and BrainVoyager and correct for vasculature-related confounders to improve the spatial accuracy of the fMRI signal. For complete details on the use and execution of this protocol, please refer to Jia et al. (2020) and Zamboni et al. (2020).This work was supported by grants to Z.K. from the Biotechnology and Biological Sciences Research Council (H012508 and BB/P021255/1), the Wellcome Trust (205067/Z/16/Z) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 840271

A protocol for ultra-high field laminar fMRI in the human brain.

Ultra-high field (UHF) neuroimaging affords the sub-millimeter resolution that allows researchers to interrogate brain computations at a finer scale than that afforded by standard fMRI techniques. Here, we present a step-by-step protocol for using UHF imaging (Siemens Terra 7T scanner) to measure activity in the human brain. We outline how to preprocess the data using a pipeline that combines tools from SPM, FreeSurfer, ITK-SNAP, and BrainVoyager and correct for vasculature-related confounders to improve the spatial accuracy of the fMRI signal. For complete details on the use and execution of this protocol, please refer to Jia et al. (2020) and Zamboni et al. (2020).This work was supported by grants to Z.K. from the Biotechnology and Biological Sciences Research Council (H012508 and BB/P021255/1), the Wellcome Trust (205067/Z/16/Z) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 840271

Recurrent Processing Drives Perceptual Plasticity.

Learning and experience are critical for translating ambiguous sensory information from our environments to perceptual decisions. Yet evidence on how training molds the adult human brain remains controversial, as fMRI at standard resolution does not allow us to discern the finer scale mechanisms that underlie sensory plasticity. Here, we combine ultra-high-field (7T) functional imaging at sub-millimeter resolution with orientation discrimination training to interrogate experience-dependent plasticity across cortical depths that are known to support dissociable brain computations. We demonstrate that learning alters orientation-specific representations in superficial rather than middle or deeper V1 layers, consistent with recurrent plasticity mechanisms via horizontal connections. Further, learning increases feedforward rather than feedback layer-to-layer connectivity in occipito-parietal regions, suggesting that sensory plasticity gates perceptual decisions. Our findings reveal finer scale plasticity mechanisms that re-weight sensory signals to inform improved decisions, bridging the gap between micro- and macro-circuits of experience-dependent plasticity

Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology

Aerobic glycolysis is a seemingly wasteful mode of ATP production that is seen both in rapidly proliferating mammalian cells and highly active contracting muscles, but whether there is a common origin for its presence in these widely different systems is unknown. To study this issue, here we develop a model of human central metabolism that incorporates a solvent capacity constraint of metabolic enzymes and mitochondria, accounting for their occupied volume densities, while assuming glucose and/or fatty acid utilization. The model demonstrates that activation of aerobic glycolysis is favored above a threshold metabolic rate in both rapidly proliferating cells and heavily contracting muscles, because it provides higher ATP yield per volume density than mitochondrial oxidative phosphorylation. In the case of muscle physiology, the model also predicts that before the lactate switch, fatty acid oxidation increases, reaches a maximum, and then decreases to zero with concomitant increase in glucose utilization, in agreement with the empirical evidence. These results are further corroborated by a larger scale model, including biosynthesis of major cell biomass components. The larger scale model also predicts that in proliferating cells the lactate switch is accompanied by activation of glutaminolysis, another distinctive feature of the Warburg effect. In conclusion, intracellular molecular crowding is a fundamental constraint for cell metabolism in both rapidly proliferating- and non-proliferating cells with high metabolic demand. Addition of this constraint to metabolic flux balance models can explain several observations of mammalian cell metabolism under steady state conditions

Detection of a two-phonon mode in a cuprate superconductor via polarimetric RIXS

Recent improvements in the energy resolution of resonant inelastic x-ray scattering experiments (RIXS) at the Cu-L$_3$ edge have enabled the study of lattice, spin, and charge excitations. Here, we report on the detection of a low intensity signal at 140meV, twice the energy of the bond-stretching (BS) phonon mode, in the cuprate superconductor $\textrm{Bi}_2\textrm{Sr}_2\textrm{Ca}\textrm{Cu}_2\textrm{O}_{8+x}$ (Bi-2212). Ultra-high resolution polarimetric RIXS measurements allow us to resolve the outgoing polarization of the signal and identify this feature as a two-phonon excitation. Further, we study the connection between the two-phonon mode and the BS one-phonon mode by constructing a joint density of states toy model that reproduces the key features of the data

Fine-scale computations for adaptive processing in the human brain

Adapting to the environment statistics by reducing brain responses to repetitive sensory information is key for efficient information processing. Yet, the fine-scale computations that support this adaptive processing in the human brain remain largely unknown. Here, we capitalise on the sub-millimetre resolution of ultra-high field imaging to examine functional magnetic resonance imaging signals across cortical depth and discern competing hypotheses about the brain mechanisms (feedforward vs. feedback) that mediate adaptive processing. We demonstrate layer-specific suppressive processing within visual cortex, as indicated by stronger BOLD decrease in superficial and middle than deeper layers for gratings that were repeatedly presented at the same orientation. Further, we show altered functional connectivity for adaptation: enhanced feedforward connectivity from V1 to higher visual areas, short-range feedback connectivity between V1 and V2, and long-range feedback occipito-parietal connectivity. Our findings provide evidence for a circuit of local recurrent and feedback interactions that mediate rapid brain plasticity for adaptive information processing

Low-energy quasi-circular electron correlations with charge order wavelength in Bi2Sr2CaCu2O8+δ\textrm{Bi}_2\textrm{Sr}_2\textrm{Ca}\textrm{Cu}_2\textrm{O}_{8+\delta}

In the study of dynamic charge order correlations in the cuprates, most high energy-resolution resonant inelastic x-ray scattering (RIXS) measurements have focused on momenta along the high-symmetry directions of the copper oxide plane. However, electron scattering along other in-plane directions should not be neglected as they may contain information relevant, for example, to the origin of charge order correlations or to our understanding of the isotropic scattering responsible for strange metal behavior in cuprates. We report high-resolution resonant inelastic x-ray scattering (RIXS) experiments that reveal the presence of dynamic electron correlations over the $q_x$-$q_y$ scattering plane in underdoped $\textrm{Bi}_2\textrm{Sr}_2\textrm{Ca}\textrm{Cu}_2\textrm{O}_{8+\delta}$ with $T_c=54$ K. We use the softening of the RIXS-measured bond stretching phonon line as a marker for the presence of charge-order-related dynamic electron correlations. The experiments show that these dynamic correlations exist at energies below approximately $70$ meV and are centered around a quasi-circular manifold in the $q_x$-$q_y$ scattering plane with radius equal to the magnitude of the charge order wave vector, $q_{CO}$. We also demonstrate how this phonon-tracking procedure provides the necessary experimental precision to rule out fluctuations of short-range directional charge order (i.e. centered around $[q_x=\pm q_{CO}, q_y=0]$ and $[q_x=0, q_y=\pm q_{CO}]$) as the origin of the observed correlations.Comment: Submitted and under revie