Biology subjects

Chacon, M.

Publications and source records attributed to Chacon, M..

10 recordsLinked to original sources

bioRxiv2026

Experimental validation of graded arithmetic and linguistic working-memory tasks using behavioral and cerebral hemodynamic measures

Graded cognitive tasks are relevant only when increasing nominal difficulty produces measurable changes in performance and a convergent physiological response. This study evaluated a five-level arithmetic paradigm and a five-level linguistic paradigm designed to engage working memory through separate exposure, retention, and response intervals. Thirty-eight healthy young adults completed both paradigms. Behavioral manipulation validity was assessed from accuracy and completion time; linguistic item-level responses were additionally modeled to detect nonlinear floor effects. Bilateral middle cerebral artery blood-flow velocity was recorded with transcranial Doppler ultrasonography. Baseline-normalized mean velocity change was the primary physiological endpoint, with positive and net area under the curve, peak response, time to peak, and early slope as secondary endpoints. Accuracy declined and completion time increased strongly across levels in both domains, with a substantially steeper accuracy decline in the linguistic paradigm. Although the levels were nominally ordered, the higher linguistic levels did not produce equidistant increases due to the ground effect. Transcranial Doppler models showed significant level-dependent changes in mean velocity, positive and net area under the curve, time to peak, and early slope. However, domain-by-level and domain-by-level-by-hemisphere interactions were not significant. Behavioral and physiological measures therefore converged mainly at the level of the graded experimental manipulation, rather than as distinct domain-specific or lateralized hemodynamic signatures. These findings lend support to paradigms as a multimodal framework for manipulating cognitive load experimentally, while also indicating upper-level language saturation and physiological quality-control decisions that should guide further improvement.

neuroscience↗

bioRxiv2026

Improved coral thermal tolerance through modulation of antioxidant defenses

Mass coral bleaching events, driven by rising ocean temperatures, are pushing reef ecosystems toward collapse on a global scale. Because oxidative stress is an early driver of coral bleaching, strategies that enhance coral antioxidant defenses may improve coral resilience under thermal stress. Here, we tested a targeted antioxidant supplementation designed to enhance oxidative stress regulation in three representative Red Sea scleractinian coral species subjected to a thermal challenge. While responses varied among species and physiological metrics, supplemented corals consistently maintained higher photophysiological performance under heat stress. In Stylophora pistillata, antioxidant supplementation was associated with enhanced catalase activity, maintenance of glutathione redox homeostasis, and lower intracellular reactive oxygen species levels. In contrast, non-fed corals exhibited oxidative imbalance, increased lipid peroxidation, and impaired photophysiological recovery, while corals receiving a non-enriched heterotrophic diet showed an intermediate response characterized by increased catalase activity but persistent glutathione oxidation and elevated ROS during recovery. Together, the dietary treatments revealed a gradient in oxidative regulation, ranging from insufficient antioxidant protection in autotrophic corals to enhanced oxidative homeostasis in antioxidant-supplemented corals. Our findings demonstrate the potential of targeted nutritional antioxidant supplementation to enhance coral oxidative regulation and physiological performance under elevated temperatures, highlighting a promising complementary approach for coral conservation and restoration efforts.

physiology↗

bioRxiv2026

Using auxotrophic donor strains to explore pQBR57 plasmid host range among environmental soil bacterial isolates

Plasmid host range (PHR) plays a key role in the spread of ecologically important genes, alongside applications in microbiome engineering, and environmental biotechnology. PHR is a complex trait arising from the combination of plasmid, donor and recipient properties. Most studies of PHR use a single donor strain, leaving the role of the donor unexplored, and often require genetically tagged recipient strains for counter selection, which limits use of non-genetically tractable strains. Here we developed a PHR screening method using auxotrophic donors that bypasses the need to genetically tag recipients, thus allowing the screening of culturable environmental bacterial strains. Specifically, we used two auxotrophic donors (P. fluorescens and P. putida), and the plasmid pQBR57-tphKAB, an environmental plasmid engineered for terephthalic acid bioremediation. We screened a library of 101 soil isolates, as potential recipients, including common soil genera of soil bacteria, Pseudomonas, Bacillus and Xanthomonas. We only observed conjugation into other Pseudomonas, but donor identity affected PHR, with P. fluorescens conjugating the plasmid into more recipient strains than P. putida. Phylogenomic analysis revealed that transconjugants clustered with P. citronellosis and P. putida lineages. In strains that were close relatives of transconjugants but who were unable to acquire the plasmid, we observed 5 defence systems not present in transconjugants that may act as barriers to plasmid acquisition. Our method provides a rapid, tag-free framework for screening PHR in environmental isolates and for investigating the influence of donor identity on plasmid conjugation.

microbiology↗

bioRxiv2025

XBP1s as a Therapeutic Target to Preserve Retinal Function During Aging and Neurodegeneration

Loss of physiological complexity, characterized by reduced adaptive multiscale coordination among system components, is increasingly recognized as a hallmark of aging and neurodegenerative disease. The retina, a window into the brain, offers a unique, accessible platform to monitor neurodegenerative disorders such as Alzheimers disease (AD). Here, we investigate the therapeutic potential of the unfolded protein response transcription factor XBP1s in preserving retinal function during aging and AD-related pathology in murine models. Using micro-electroretinography with multielectrode arrays, we recorded retinal responses to chirp and white noise stimuli in four mouse models: wild-type (WT), XBP1s-overexpressing (TgXBP1s), AD model (5xFAD), and their crossbreed (TgXBP1s/5xFAD) at approximately 3 and 7 months of age. We assessed retinal signals through entropy-based complexity measures and wavelet coherence between stimulus and response. While WT and 5xFAD mice exhibited age-related decline in retinal complexity, TgXBP1s and TgXBP1s/5xFAD mice maintained higher complexity levels and increased Wcoh in adulthood, indicating functional preservation. These results demonstrate that sus-tained XBP1s expression protects retinal electrophysiological integrity and highlight the retinas value as a scalable, noninvasive biomarker platform to evaluate therapeutic efficacy targeting neurodegenerative mechanisms.

neuroscience↗

bioRxiv2025

Observing Grazing Behavior Transitions in Cafeteria roenbergensis with Video-Rate Two-Photon Microscopy

Grazing behavior of free-living aquatic heterotrophic nanoflagellates (HNFs) on bacteria plays a central role in shaping microbial community structure and nutrient cycling. However, direct observation of these interactions has been limited by the rapid motility of flagellates and the transient nature of predator-prey encounters. To address this gap, this study presents a novel application of video-rate two-photon fluorescence microscopy for high resolution, real-time imaging of fast-moving microorganisms. HNF Cafeteria roenbergensis is used as a model system to investigate dynamic grazing interactions between fluorescently stained bacteria and the flagellates, where the flagellates are detected via their intrinsic cellular autofluorescence. This two-photon microscope combined with real-time imaging capability enables continuous capture of contact, capture, ingestion, and digestion steps during grazing. Quantitative analysis across varying prey concentration reveals phase-specific durations and saturation behavior in grazing activities. Furthermore, transitions in grazing dynamics across two continuous periods of flagellates in starved and fed conditions are observed in live time series videos. This technique provides a powerful new tool to study rapid microbial interactions in situ and can be broadly applicable to diverse microbe-microbe systems. With the integration of targeted fluorescent molecular probes, this technique holds significant potential for uncovering mechanical and biochemical interactions underlying microbial feeding and communication. SignificanceThis study significantly advances microbial ecology by applying video-rate two-photon fluorescence microscopy to directly visualize and quantify the rapid grazing behavior of flagellates on bacteria. By enabling real-time observation of contact, ingestion, and digestion during the grazing events, the technique overcomes limitations of traditional imaging. It captures behavioral transitions tied to physiological states, offering quantitative insight into microbial predator-prey dynamics. This method establishes a broadly applicable platform for studying fast, transient microbial interactions. Although current limitations include the lack of 3D tracking, emerging optical technologies promise enhanced capabilities, paving the way for deeper understanding of microbial processes in aquatic ecosystems.

biophysics↗

bioRxiv2025

Damage-induced phosphorylation of BRC-1/BRD-1 in meiosis preserves germline integrity

Multiple DNA repair pathways have evolved to safeguard genome integrity and ensure organismal viability in the face of DNA damage. Errors in DNA repair processes in meiosis can lead to aneuploidy and developmental defects, but the processes that protect the germline from DNA damage remain poorly understood. Here we report a DNA damage-induced phosphorylation of the BRC-1/BRD-1 heterodimer that is essential for germline integrity in C. elegans. Failure to phosphorylate BRC-1/BRD-1 in response to DNA damage results in meiotic DSBs accumulation, chromosome breakage, catastrophic diakinesis and loss of fecundity. We further show that these defects are driven by the activity of C. elegans Bloom and Mus81, which catalyse Holliday junction dissolution and resolution, respectively. Hence, we propose that phosphorylation of BRC-1/BRD-1 in response to excess meiotic DSBs constitutes a key regulatory step that ensures the proper resolution of recombination intermediates required to preserve germline integrity.

molecular biology↗

bioRxiv2024

Tuning the performance of a TphR-based terephthalate biosensor with a design of experiments approach

Transcription factor-based biosensors are genetic tools that aim to predictability link the presence of a specific input stimuli to a tailored gene expression output. The performance characteristics of a biosensor fundamentally determines its potential applications. However, current methods to engineer and optimise tailored biosensor responses are highly nonintuitive, and struggle to investigate multidimensional sequence/design space efficiently. In this study we employ a design of experiments (DoE) approach to build a framework for efficiently engineering activator-based biosensors with tailored performances, and we apply the framework for the development of biosensors for the polyethylene terephthalate (PET) plastic degradation monomer terephthalate (TPA). We simultaneously engineer the core promoter and operator regions of the responsive promoter, and by employing a dual refactoring approach, we were able to explore an enhanced biosensor design space and assign their causative performance effects. The approach employed here serves as a foundational framework for engineering transcriptional biosensors and enabled development of tailored biosensors with enhanced dynamic range and diverse signal output, sensitivity, and steepness. We further demonstrate its applicability on the development of tailored biosensors for primary screening of PET hydrolases and enzyme condition screening, demonstrating the potential of statistical modelling in optimizing biosensors for tailored industrial and environmental applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/600737v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@2db5d6org.highwire.dtl.DTLVardef@fd0935org.highwire.dtl.DTLVardef@67a01dorg.highwire.dtl.DTLVardef@140da62_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract. Employment of a DoE framework for fine-tuning biosensor performance. C_FIG HighlightsO_LIBioinformatic mining of allosteric transcription factors to produce TPA biosensors C_LIO_LIEfficient sampling of complex sequence-function relationships of genetic circuits C_LIO_LIModelling to learn and optimise biosensor genetic circuits C_LIO_LIApplication of biosensors for primary and secondary enzyme screening applications C_LI

synthetic biology↗

bioRxiv2023

Degradation and bioconversion of complex municipal solid waste streams into human biotherapeutics and biopolymers

The use of biomass and organic waste as a feedstock for the production of fuels, chemicals and materials offers great potential to support the transition to net-zero and circular economic models. However, such renewable feedstocks are often complex, highly heterogeneous, and subject to geographical and seasonal variability, creating supply-chain inconsistency that impedes adoption. Towards addressing these challenges, the development of engineered microorganisms equipped with the ability to flexibly utilise complex, heterogenous substrate compositions for growth and bio-production would be greatly enabling. Here we show through careful strain selection and metabolic engineering, that Pseudomonas putida can be employed to permit efficient co-utilisation of highly heterogeneous substrate compositions derived from hydrolysed mixed municipal-like waste fractions, with remarkable resilience to compositional variability. To further illustrate this, one pot enzymatic pre-treatments of the five most abundant, hydrolytically labile, mixed waste feedstocks was performed - including food, plastic, organic, paper and cardboard, and textiles - for growth and synthesis of exemplar bio-products by engineered P. putida. Finally, prospective life cycle assessment and life cycle costing illustrated the climate change and economic advantage, respectively, of using the waste-derived feedstock for biomanufacturing compared to conventional waste treatment options. This work demonstrates the potential for expanding the treatment strategies for mixed municipal waste to include engineered microbial bio-production platforms that can accommodate variability in feedstock inputs to synthesise a range of chemical and material outputs.

synthetic biology↗

bioRxiv2022

Multiscale Entropy Analysis of Retinal Signals Reveals Reduced Complexity in a Mouse Model of Alzheimer's Disease

Alzheimers disease (AD) is one of the most significant health challenges of our time, affecting a growing number of the elderly population. In recent years, the retina has received increased attention as a candidate for AD biomarkers since it appears to manifest the pathological signatures of the disease. Therefore, its electrical activity may hint at AD-related physiological changes. However, it is unclear how AD affects retinal electrophysiology and what tools are more appropriate to detect these possible changes. In this study, we used entropy tools to estimate the complexity of the dynamics of healthy and diseased retinas at different ages. We recorded microelectroretinogram responses to visual stimuli of different nature from retinas of young and adult, wild-type and 5xFAD -an animal model of AD- mice. To estimate the complexity of signals, we used the multiscale entropy approach, which calculates the entropy at several time scales using a coarse graining procedure. We found that young retinas had more complex responses to different visual stimuli. Further, the responses of young, wild-type retinas to natural-like stimuli exhibited significantly higher complexity than young, 5xFAD retinas. Our findings support a theory of complexity-loss with aging and disease and can have significant implications for early AD diagnosis.

neuroscience↗

bioRxiv2021

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods. ImportanceEnvironmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made towards containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) [1], a large-scale environmental monitoring effort in elementary school and child care settings, has processed > 13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT - qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.

microbiology↗