Integrative metabolomics to identify molecular signatures of responses to vaccines and infections

Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to the emergence of immunometabolism, an important area of study, as leukocytes generate and are impacted by key metabolites important to innate and adaptive immunity. Herein, we discuss the metabolomic signatures and pathways perturbed by the activation of the human immune system during infection and vaccination. For example, infection induces changes in lipid (e.g., free fatty acids, sphingolipids, and lysophosphatidylcholines) and amino acid pathways (e.g., tryptophan, serine, and threonine), while vaccination can trigger changes in carbohydrate and bile acid pathways. Amino acid, carbohydrate, lipid, and nucleotide metabolism is relevant to immunity and is perturbed by both infections and vaccinations. Metabolomics holds substantial promise to provide fresh insight into the molecular mechanisms underlying the host immune response. Its integration with other systems biology platforms will enhance studies of human health and disease

Optimization and Control of Agent-Based Models in Biology: A Perspective

Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of analyzing and using ABMs, due to the lack of the type of mathematical tools available for more traditional models, which leaves simulation as the primary approach. As models become large, simulation becomes challenging. This paper proposes a novel approach to two mathematical aspects of ABMs, optimization and control, and it presents a few first steps outlining how one might carry out this approach. Rather than viewing the ABM as a model, it is to be viewed as a surrogate for the actual system. For a given optimization or control problem (which may change over time), the surrogate system is modeled instead, using data from the ABM and a modeling framework for which ready-made mathematical tools exist, such as differential equations, or for which control strategies can explored more easily. Once the optimization problem is solved for the model of the surrogate, it is then lifted to the surrogate and tested. The final step is to lift the optimization solution from the surrogate system to the actual system. This program is illustrated with published work, using two relatively simple ABMs as a demonstration, Sugarscape and a consumer-resource ABM. Specific techniques discussed include dimension reduction and approximation of an ABM by difference equations as well systems of PDEs, related to certain specific control objectives. This demonstration illustrates the very challenging mathematical problems that need to be solved before this approach can be realistically applied to complex and large ABMs, current and future. The paper outlines a research program to address them

Patients With Generalized Joint Hypermobility Have Thinner Superior Hip Capsules and Greater Hip Internal Rotation on Physical Examination

PURPOSE: To compare preoperative hip range of motion (ROM), hip capsular thickness on magnetic resonance imaging (MRI), and bony morphology on radiographs and computed tomography (CT) between patients with and without joint hypermobility as measured by the Beighton Test score (BTS), with subanalysis based on sex and age. METHODS: Consecutive patients who underwent hip arthroscopy for a diagnosis of femoroacetabular impingement syndrome with or without dysplasia were retrospectively reviewed. Patient BTS, hip ROM, demographics, surgical data, morphologic measures on radiographs and CT, and MRI findings including hip capsule thickness at various locations were compiled. Multiple statistical tests were performed, including multivariable linear or logistic regression models, while controlling for BTS, age, and sex. RESULTS: In total, 99 patients were included with a mean age of 29 ± 9.9 years; 62 (62.6%), were female. Forty patients (40.4%) had a BTS ≥4. Female patients (P \u3c .001) and younger patients (26.7 vs 30.9 years, P = .030) were more likely to have a BTS ≥4. Male patients had significantly thicker superior capsules (3.4 mm vs. 2.8 mm, P = .034). BTS was not associated with capsular thickness when controlling for sex. On CT, femoral version (18.9° vs 11.4°, P \u3c .001), and McKibben index (37.8° vs. 28.2°, P \u3c .001) were significantly greater in those with a BTS ≥4. Patients with a BTS ≥4 had more hip internal rotation at 90° of flexion (15.0° vs 10.0°, P \u3c .001), when prone (30.0° vs 20.0°, P = .004), and in extension (10.0° vs. 5.0°, P \u3c .001). CONCLUSIONS: All female patients, regardless of Beighton score, and all patients with a BTS ≥4 indicated for primary hip arthroscopy for femoroacetabular impingement syndrome with or without dysplasia were more likely to have thinner superior hip capsules on MRI and greater hip internal rotation on exam. Bony morphologic differences exist between sexes and between patients with and without hypermobility, likely contributing to differences in ROM. LEVEL OF EVIDENCE: III, retrospective cohort study

Breakfast glycaemic index and exercise: combined effects on adolescents' cognition

The aim of the present study was to examine the combined effects of breakfast glycaemic index (GI) and a mid-morning bout of exercise on adolescents’ cognitive function. Participants were randomly allocated to a high or low GI breakfast group in a mixed research design, where each participant completed two experimental trials (exercise and resting). Forty-two adolescents (12.4±0.5 years old), undertook a bout of exercise (ten repeats of level one of the multi-stage fitness test; exercise trial) or continued to rest (resting trial) following consumption of either a high or low GI breakfast. A battery of cognitive function tests (visual search test, Stroop test and Sternberg paradigm) was completed 30 min before and 45 min following the exercise. Average heart rate during exercise was 170±15 beats.min-1. On the complex level of the Stroop test, response times improved across the morning following the low GI breakfast on both the exercise and resting trials, though the improvement was greatest on the exercise trial. However, response times only improved on the resting trial following the high GI breakfast (p = 0.012). On the 5 letter level of the Sternberg paradigm, response times improved across the morning following the low GI breakfast (regardless of exercise) and only on the exercise trial following the high GI breakfast (p = 0.019). The findings of the present study suggest that the combined effects of breakfast GI and exercise in adolescents depend upon the component of cognitive function examined. A low GI breakfast and mid-morning bout of exercise were individually beneficial for response times on the Sternberg paradigm, whereas they conferred additional benefits for response times on the Stroop test

Nationally Representative Estimates of Serum Testosterone Concentration in Never-Smoking, Lean Men Without Aging-Associated Comorbidities

Context Testosterone deficiency prevalence increases with age, comorbidities, and obesity. Objective To inform clinical guidelines for testosterone deficiency management and development of targets for nonpharmacologic intervention trials for these men, we determined serum testosterone in never-smoking, lean men without select comorbidities in nationally representative surveys. Design Setting Participants We used cross-sectional data for never-smoking, lean men ≥20 years without diabetes, myocardial infarction, congestive heart failure, stroke, or cancer, without use of hormone-influencing medications, and participated in morning sessions of National Health and Nutrition Examination Survey (NHANES) III (phase I 1988-1991) or continuous NHANES (1999-2004). By age, we determined median total testosterone (ng/mL) measured previously by a Food and Drug Administration-approved immunoassay and median estimated free testosterone concentration. Results In NHANES III, in never-smoking, lean men without comorbidities, median (25th, 75th percentile) testosterone was 4% to 9% higher than all men-20 to 39 years: 6.24 (5.16, 7.51), 40 to 59: 5.37 (3.83, 6.49), and ≥60: 4.61 (4.01, 5.18). In continuous NHANES, in never-smoking, lean men without comorbidities, levels were 13% to 24% higher than all men-20 to 39 years: 6.26 (5.32, 7.27), 40 to 59: 5.86 (4.91, 6.55), and ≥60: 4.22 (3.74, 5.73). In never-smoking, lean men without comorbidities, median estimated free testosterone was similar to (NHANES III) or slightly higher than (continuous NHANES) in all men. Conclusions These nationally representative data document testosterone levels (immunoassay) in never-smoking, lean men without select comorbidities 30 and 15 to 20 years ago. This information can be incorporated into guidelines for testosterone deficiency management and used to develop targets for nonpharmacologic intervention trials for testosterone deficiency

Import of cytochrome c into mitochondria

The import of cytochrome c into mitochondria can be resolved into a number of discrete steps. Here we report on the covalent attachment of heme to apocytochrome c by the enzyme cytochrome c heme lyase in mitochondria from Neurospora crassa. A new method was developed to measure directly the linkage of heme to apocytochrome c. This method is independent of conformational changes in the protein accompanying heme attachment. Tryptic peptides of [35S]cysteine-labelled apocytochrome c, and of enzymatically formed holocytochrome c, were resolved by reverse-phase HPLC. The cysteine-containing peptide to which heme was attached eluted later than the corresponding peptide from apocytochrome c and could be quantified by counting 35S radioactivity as a measure of holocytochrome c formation. Using this procedure, the covalent attachment of heme to apocytochrome c, which is dependent on the enzyme cytochrome c heme lyase, could be measured. Activity required heme (as hemin) and could be reversibly inhibited by the analogue deuterohemin. Holocytochrome c formation was stimulated 5–10-fold by NADH > NADPH > glutathione and was independent of a potential across the inner mitochondrial membrane. NADH was not required for the binding of apocytochrome c to mitochondria and was not involved in the reduction of the cysteine thiols prior to heme attachment. Holocytochrome c formation was also dependent on a cytosolic factor that was necessary for the heme attaching step of cytochrome c import. The factor was a heat-stable, protease-insensitive, low-molecular-mass component of unknown function. Cytochrome c heme lyase appeared to be a soluble protein located in the mitochondrial intermembrane space and was distinct from the previously identified apocytochrome c binding protein having a similar location. A model is presented in which the covalent attachment of heme by cytochrome c heme lyase also plays an essential role in the import pathway of cytochrome c

The Neurokinin 1 Receptor Antagonist, Ezlopitant, Reduces Appetitive Responding for Sucrose and Ethanol

Abstract Background: The current obesity epidemic is thought to be partly driven by over-consumption of sugar-sweetened diets and soft drinks. Loss-of-control over eating and addiction to drugs of abuse share overlapping brain mechanisms including changes in motivational drive, such that stimuli that are often no longer ‘liked’ are still intensely ‘wanted’ [7,8]. The neurokinin 1 (NK1) receptor system has been implicated in both learned appetitive behaviors and addiction to alcohol and opioids; however, its role in natural reward seeking remains unknown. Methodology/Principal Findings: We sought to determine whether the NK1-receptor system plays a role in the reinforcing properties of sucrose using a novel selective and clinically safe NK1-receptor antagonist, ezlopitant (CJ-11,974), in three animal models of sucrose consumption and seeking. Furthermore, we compared the effect of ezlopitant on ethanol consumption and seeking in rodents. The NK1-receptor antagonist, ezlopitant decreased appetitive responding for sucrose more potently than for ethanol using an operant self-administration protocol without affecting general locomotor activity. To further evaluate the selectivity of the NK1-receptor antagonist in decreasing consumption of sweetened solutions, we compared the effects of ezlopitant on water, saccharin-, and sodium chloride (NaCl) solution consumption. Ezlopitant decreased intake of saccharin but had no effect on water or salty solution consumption. Conclusions/Significance: The present study indicates that the NK1-receptor may be a part of a common pathway regulating the self-administration, motivational and reinforcing aspects of sweetened solutions, regardless of caloric value, and those of substances of abuse. Additionally, these results indicate that the NK1-receptor system may serve as a therapeutic target for obesity induced by over-consumption of natural reinforcers

The Astropy Project: Building an inclusive, open-science project and status of the v2.0 core package

The Astropy project supports and fosters the development of open-source and openly-developed Python packages that provide commonly-needed functionality to the astronomical community. A key element of the Astropy project is the core package Astropy, which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of inter-operable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy project