Biology subjects

Palacios, D.

Publications and source records attributed to Palacios, D..

3 recordsLinked to original sources

bioRxiv2026

AMMPER-2: A spatially explicit agent-based model of microbial radiobiology with redox dye simulation

To reduce health risks for human space exploration, it is important to model the effects of deep-space radiation on biological systems. The budding yeast Saccharomyces cerevisiae is a common model organism in space radiobiology, but little is known about how radiation damage to individual cells translates into the population-level effects that experiments measure. The Agent-Based Model for Microbial Populations Exposed to Radiation (AMMPER) is a spatially explicit agent-based model that simulates the effects of ionizing radiation on S. cerevisiae cells and produces population-level results. Its goal is to improve experiment design and data interpretation. AMMPER-1 demonstrated that agent-based simulations can qualitatively reproduce the effects of proton radiation on the growth rate of wild-type and DNA-repair mutant yeast. Here, we present AMMPER-2, which addresses limitations of the first model and expands its capabilities. AMMPER-2 incorporates the dynamics of the redox dye alamarBlue, a data type commonly generated in spaceflight microbiology experiments, and models the fate of reactive oxygen species in more detail. It also adds an improved graphical interface and runs faster. AMMPER-2 remains easy to execute in Python on a standard personal laptop, providing space biologists a tool to explore experimental conditions, generate hypotheses, and interpret data from microbial space radiation experiments.

microbiology↗

bioRxiv2023

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in Anza Borrego Desert

Here we describe the metagenome composition, community functional annotation, and diversity of prokaryotic microbial species derived from calcareous stromatolite formations discovered in the dry stream bed of the open-canopy, ephemeral San Felipe Creek in the Anza Borrego Desert. In this environment, resident microbes must be able to adapt to the harsh conditions of extreme heat, high UV light, desiccation and fluctuating solubilization/precipitation and hydration/evaporation. Metagenomic analysis revealed a community capable of carrying out complete nitrogen fixation and assimilatory nitrate reduction, forming biofilms and quorum sensing, and potentially forming thick-walled akinetes as desiccation-resistant stages. Nitrogen cycling is likely to play a fundamental role in mediating both the structure of the stromatolite microbial community and the mineral precipitation/dissolution. The viruses present in the stromatolites, particularly Nodularia and Mycobacterium phages are also likely to impact community population dynamics and activity. Stromatolite community members possess different morphological and physiological strategies to cope with desiccation stress. Metagenomic signatures were found for scytonemin, carotenoids, synthesis of potential microsporine-like amino acids; genes involved in microalgal desiccation tolerance, including those encoding aquaporins, chaperones, antioxidants; and enzymes responsible for the synthesis of trehalose, sucrose, and polyamines. The stromatolite ecosystem provides a diverse array of microniches where different functional guilds can develop complex metabolite exchange with the substrate supporting their life in extreme conditions. Metagenome analyses revealed several genes that might enable a specialized and unique group of endolithic cyanobacteria including Chroococcidiopsis, Hyella, Myxosarcina, and Pleurocapsa to derive metals and important nutrients from rocks, being potentially destructive for the calcareous formations. Our study revealed environmental adaptations of freshwater microbial communities in desert stream stromatolites which may provide valuable insights into Precambrian paleoenvironments, which are little known.

genomics↗

bioRxiv2019

The effect of dopamine transporter blockade on optical self-stimulation: behavioral and computational evidence for parallel processing in brain reward circuitry

The neurobiological study of reward was launched by the discovery of intracranial self-stimulation (ICSS). Subsequent investigation of this phenomenon provided the initial link between reward-seeking behavior and dopaminergic neurotransmission. We re-evaluated this relationship by psychophysical, pharmacological, optogenetic, and computational means. In rats working for direct, optical activation of midbrain dopamine neurons, we varied the strength and opportunity cost of the stimulation and measured time allocation, the proportion of trial time devoted to reward pursuit. We found that the dependence of time allocation on the strength and cost of stimulation was similar formally to that observed when electrical stimulation of the medial forebrain bundle served as the reward. When the stimulation is strong and cheap, the rats devote almost all their time to reward pursuit; time allocation falls off as stimulation strength is decreased and/or its opportunity cost is increased. A 3D plot of time allocation versus stimulation strength and cost produces a surface resembling the corner of a plateau (the "reward mountain"). We show that dopamine-transporter blockade shifts the mountain along both the strength and cost axes in rats working for optical activation of midbrain dopamine neurons. In contrast, the same drug shifted the mountain uniquely along the opportunity-cost axis when rats worked for electrical MFB stimulation in a prior study. Dopamine neurons are an obligatory stage in the dominant model of ICSS, which positions them at a key nexus in the final common path for reward seeking. This model fails to provide a cogent account for the differential effect of dopamine transporter blockade on the reward mountain. Instead, we propose that midbrain dopamine neurons and neurons with non-dopaminergic, MFB axons constitute parallel limbs of brain-reward circuitry that ultimately converge on the final-common path for the evaluation and pursuit of rewards. Author summaryTo succeed in the struggle for survival and reproductive success, animals must make wise choices about which goals to pursue and how much to pay to attain them. How does the brain make such decisions and adjust behaviour accordingly? An animal model that has long served to address this question entails delivery of rewarding brain stimulation. When the probe is positioned appropriately in the brain, rats will work indefatigably to trigger such stimulation. Dopamine neurons play a crucial role in this phenomenon. The dominant model of the brain circuitry responsible for the reward-seeking behavior treats these cells as a gateway through which the reward-generating brain signals must pass. Here, we challenge this idea on the basis of an experiment in which the dopamine neurons were activated selectively and directly. Mathematical modeling of the results argues for a new view of the structure of brain reward circuitry. On this view, the pathway(s) in which the dopamine neurons are embedded is one of a set of parallel channels that process reward signals in the brain. To achieve a full understanding of how goals are evaluated, selected and pursued, the full set of channels must be identified and investigated.

neuroscience↗