PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways.

BACKGROUND: Metabolic pathways support the enzyme flux that converts input chemicals into energy and cellular building blocks. With a constant rate of input, steady-state flux is achieved when metabolite concentrations and reaction rates remain constant over time. Individual genes undergo mutation, while selection acts on higher level functions of the pathway, such as steady-state flux where applicable. Modeling the evolution of metabolic pathways through mechanistic sets of ordinary differential equations is a piece of the genotype-phenotype map model for interpreting genetic variation and inter-specific differences. Such models can generate distinct compensatory changes and adaptive changes from directional selection, indicating single nucleotide polymorphisms and fixed differences that could affect phenotype. If used for inference, this would ultimately enable detection of selection on metabolic pathways as well as inference of ancestral states for metabolic pathway function. RESULTS: A software tool for simulating the evolution of metabolic pathways based upon underlying biochemistry, phylogenetics, and evolutionary considerations is presented. The Python program, Phylogenetic Evolution of Metabolic Pathway Simulator (PEMPS), implements a mutation-selection framework to simulate the evolution of the pathway over a phylogeny by interfacing with COPASI to calculate the steady-state flux of the metabolic network, introducing mutations as alterations in parameter values according to a model, and calculating a fitness score and corresponding probability of fixation based on the change in steady-state flux value(s). Results from simulations are consistent with a priori expectations of fixation probabilities and systematic change in model parameters. CONCLUSIONS: The PEMPS program simulates the evolution of a metabolic pathway with a mutation-selection modeling framework based on criteria like steady-state flux that is designed to work with SBML-formatted kinetic models, and Newick-formatted phylogenetic trees. The Python software is run on the Linux command line and is available at https://github.com/nmccloskey/PEMPS .

Role of α1-GABAA receptors in the serotonergic dorsal raphe nucleus in models of opioid reward, anxiety, and depression.

BACKGROUND: The serotonin (5-hydroxytryptamine (5-HT))-mediated system plays an important role in stress-related psychiatric disorders and substance abuse. Our previous studies showed that stress and drug exposure can modulate the dorsal raphe nucleus (DRN)-5-HT system via γ-aminobutyric acid (GABA)A receptors. Moreover, GABAA receptor-mediated inhibition of serotonergic DRN neurons is required for stress-induced reinstatement of opioid seeking. AIM/METHODS: To further test the role of GABAA receptors in the 5-HT system in stress and opioid-sensitive behaviors, our current study generated mice with conditional genetic deletions of the GABAA α1 subunit to manipulate GABAA receptors in either the DRN or the entire population of 5-HT neurons. The GABAA α1 subunit is a constituent of the most abundant GABAA subtype in the brain and the most highly expressed subunit in 5-HT DRN neurons. RESULTS: Our results showed that mice with DRN-specific knockout of α1-GABAA receptors exhibited a normal phenotype in tests of anxiety- and depression-like behaviors as well as swim stress-induced reinstatement of morphine-conditioned place preference. By contrast, mice with 5-HT neuron-specific knockout of α1-GABAA receptors exhibited an anxiolytic phenotype at baseline and increased sensitivity to post-morphine withdrawal-induced anxiety. CONCLUSIONS: Our data suggest that GABAA receptors on 5-HT neurons contribute to anxiety-like behaviors and sensitivity of those behaviors to opioid withdrawal.

Sex differences in ethanol consumption and drinking despite negative consequences following adolescent social isolation stress in male and female rats.

Alcohol use disorder (AUD) is a debilitating psychiatric disorder characterized by drinking despite negative social and biological consequences. AUDs make up 71% of substance use disorders, with relapse rates as high as 80%. Current treatments stem from data conducted largely in males and fail to target the psychological distress motivating drinking in stress-vulnerable and at-risk populations. Here we employed a rat model and hypothesized that early life stress would reveal sex differences in ethanol intake and drinking despite negative consequences in adulthood. Rats were group housed or isolated postweaning to evaluate sex and stress effects on ethanol consumption in homecage drinking, self-administration (SA), and punished SA (drinking despite negative consequences) in adulthood. Stressed rats showed elevated homecage ethanol intake, an effect more pronounced in females. During SA, males were more sensitive to stress-induced elevations of drinking over time, but females drank more overall. Stressed rats, regardless of sex, responded more for ethanol than their non-stressed counterparts. Stressed females showed greater resistance to punishment-suppressed SA than stressed males, indicating a more stress-resistant drinking phenotype. Results support our hypothesis that adolescent social isolation stress enhances adult ethanol intake in a sex- and model-dependent manner with females being especially sensitive to early life stress-induced elevations in ethanol intake and punished SA in adulthood. Our findings echo the clinical literature which indicates that stress-vulnerable populations are more likely to 'self-medicate' with substances. Elucidating a potential mechanism that underlies why vulnerable populations 'self-medicate' with alcohol can lead towards developing catered pharmacotherapeutics that could reduce punishment-resistant drinking and relapse.

Paradoxical anxiolytic effect of the 'bath salt' synthetic cathinone MDPV during early abstinence is inhibited by a chemokine CXCR4 or CCR5 receptor antagonist.

Chemokine CXCR4 and CCR5 receptors are best known as HIV co-entry receptors, but evidence that CXCR4 or CCR5 blockade reduces rewarding and locomotor-stimulant effects of psychostimulants in rats suggests a role in psychostimulant use disorders. We investigated the impact of CXCR4 or CCR5 receptor antagonism on anxiety-related effects of the synthetic cathinone 3,4-methylenedioxypyrovalerone (MDPV) in the elevated zero-maze (EZM) assay. Rats exposed to a 4-day MDPV binge dosing paradigm and tested 24 or 72 h post-treatment spent more time in the open compartment at the 24-h time point but less time at the 72-h post-binge time point. Daily administration of AMD 3100, a CXCR4 antagonist (10 mg/kg), or maraviroc, a CCR5 antagonist (2.5 mg/kg), during MDPV treatment inhibited the MDPV-induced increase in time spent in the open compartment. Neither antagonist affected the MDPV-induced reduction in time spent in the open compartment at the 72-h post-binge time point. Cocaine, administered in the same paradigm as MDPV, did not increase time spent in the open compartment 24-h post-binge, suggesting specificity to MDPV. The present results identify a surprising anxiolytic-like effect of MDPV 24 h after cessation of repeated exposure that is sensitive to chemokine CXCR4 and CCR5 receptor activity.