Biology subjects

Escobar, A.

Publications and source records attributed to Escobar, A..

7 recordsLinked to original sources

bioRxiv2026

Criticality-related dynamics accompany long-term functional decline in primary cortical MEA cultures

Primary cortical neuron cultures are widely used to study network development and decline, but their long-term electrophysiological trajectories are poorly characterized. We used multi-electrode arrays to longitudinally monitor Wistar rat cortical cultures for up to ~730 days in vitro (DIV), combining activity measures with survival analysis and criticality metrics. Wells shared an early developmental phase, with mean firing rate peaking at 12-14 Hz around DIV 100-150, before diverging into two phenotypes: early-death wells, showing progressive loss of burst organization, longer inter-burst intervals, shorter bursts, and steep declines in active-electrode recruitment; and long-survival wells, which sustained organized bursting and measurable activity well beyond DIV 400, in some cases past DIV 700. Cox proportional-hazards modeling with FDR correction across thirteen candidate features identified burst duration, inter-burst interval, synchrony, mean firing rate, branching ratio, and Kappa index as significant predictors of time to network failure. Criticality metrics offered the most mechanistic insight: in early-death wells, branching ratio declined toward zero and Kappa index rose toward its upper bound as networks approached silencing. Beyond their average levels, the rate of change of branching ratio and Kappa index over recordings was the strongest correlate of survival time among all criticality metrics. Neuronal avalanche size and duration exponents and their scaling relation, remained consistent with scale-free dynamics in both phenotypes while networks were active, though avalanche occurrence rate declined progressively in early-death wells without reaching significance as an independent predictor. These results show that long-term network survival is not determined by firing rate alone, but by preserved burst organization, sustained electrode recruitment and near-critical propagation dynamics. This work offers one of the longest electrophysiological characterizations of rodent cortical cultures to date and identifies criticality-based metrics as promising tools for predicting network decline and evaluating interventions to preserve long-term neuronal function.

neuroscience↗

bioRxiv2026

Polymicrobial-driven NLRP6 inflammasome regulates IL-1β production and alveolar bone loss in a murine model of periodontitis

Periodontal disease is a chronic inflammatory condition that develops in response to oral microbiome dysbiosis and host-microbiome immune response dysregulation. The innate immune system plays a major role in the development and persistence of disease in part by producing inflammatory cytokines. One of the major cytokines implicated in disease is interleukin-1{beta} (IL-1{beta}), which requires inflammasome activation. Much of the oral microbiome, including Streptococci, which are otherwise considered commensal, is required for the full development of periodontal disease. We have previously reported that inflammatory-activated macrophages and neutrophils counterintuitively allow survival of internalized Streptococcus gordonii over non-activated phagocytes. This internal bacterial survival leads to inflammasome activation via the cytoplasmic activator NLRP6, but not NLRP3, and subsequent increases in IL-1{beta} release. Here, we test and find that the keystone pathogen Porphyromonas gingivalis can activate macrophages in a manner that allows for increased S. gordonii survival and IL-1{beta} production above levels when P. gingivalis interacts with macrophages alone. We also use the mouse ligature-induced periodontal disease model to test the importance of NLRP6 in disease development. We found mice lacking NLRP6 had significantly reduced bone loss, IL-1{beta}, and neutrophil infiltration following disease induced by P. gingivalis when S. gordonii or other mouse commensals were present, but had no effect when S. gordonii was inoculated alone. This work thus reveals an additional important inflammasome activation mechanism by which oral keystone pathogens may stimulate periodontal disease progression.

immunology↗

bioRxiv2026

Expanding Threat of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae in Peru: Genomic and Phenotypic Evidence of High-Risk Clones Dissemination

Carbapenemase-producing Enterobacterales represent a growing global threat due to their extensive antimicrobial resistance and rapid dissemination. This study characterized the phenotypic and genomic features of Escherichia coli and Klebsiella pneumoniae isolates collected between 2020 and 2022 from four healthcare institutions in Lima, Peru. A total of 320 non-redundant isolates (61 E. coli and 259 K. pneumoniae) were analyzed through antimicrobial susceptibility testing, polymerase chain reaction, and whole-genome sequencing. The most frequent carbapenemase gene was blaNDM (69%), followed by blaKPC (16.9%) and blaOXA-48-like (4.6%). Eleven K. pneumoniae isolates co-produced NDM and KPC, and one E. coli isolate co-harbored NDM and OXA-48-like. All isolates were multidrug resistant, and 5% were pandrug resistant. Novel {beta}-lactam/{beta}-lactamase inhibitor combinations such as aztreonam/avibactam and cefiderocol showed complete activity against all classes of carbapenemases. Genomic analysis revealed predominant E. coli sequence types ST167 and ST410 and K. pneumoniae lineages ST147, ST15, ST45, and ST273. The blaNDM-5 allele was detected for the first time in Peru, mostly in E. coli ST167, carried on multireplicon IncF-type plasmids. In K. pneumoniae, ST147 was identified as a dominant clone associated with blaNDM-1, indicating sustained local dissemination of high-risk clonal groups. The coexistence of multiple carbapenemases and plasmid backbones highlights the ongoing evolution of resistance mechanisms. These findings provide actionable evidence to guide treatment strategies in settings with high prevalence of metallo-{beta}-lactamases and underscores the need for continuous genomic surveillance and antimicrobial stewardship to mitigate their clinical and epidemiological impact.

microbiology↗

bioRxiv2022

Transmembrane 163 (TMEM163) protein interacts with specific mammalian SLC30 zinc efflux transporter family members

Recently, we reported that TMEM163 is a zinc efflux transporter that likely belongs to the mammalian solute carrier 30 (Slc30/ZnT) subfamily of the cation diffusion facilitator (CDF) protein superfamily. We hypothesized that human TMEM163 forms functional heterodimers with ZNT proteins based on their subcellular localization overlapping with TMEM163 and previous reports that certain ZNT monomers interact with each other. In this study, we heterologously expressed individual constructs with a unique peptide tag containing TMEM163, ZNT1, ZNT2, ZNT3, and ZNT4 (negative control) or co-expressed TMEM163 with each ZNT in HEK-293 cells for co-immunoprecipitation (co-IP) experiments. We also co-expressed TMEM163 with two different peptide tags as a positive co-IP control. Western blot analyses revealed that TMEM163 dimerizes with itself but that it also heterodimerizes with ZNT1, ZNT2, ZNT3, and ZNT4 proteins. Native co-IP using mouse tissues confirmed the interactions while confocal microscopy revealed that TMEM163 and ZNT proteins partially co-localize in cells, suggesting that they exist as homodimers and heterodimers in their respective subcellular sites. Functional zinc flux assays using Fluozin-3 and Newport Green dyes show that cells expressing TMEM163 homodimers extruded zinc slightly less efficiently than cells expressing TMEM163/ZNT heterodimers. Cell surface biotinylation revealed a subtle change in the plasma membrane localization of TMEM163 upon co-expression with certain ZNT proteins, which possibly explains why zinc efflux is marginally different for TMEM163 homodimers than TMEM163/ZNT heterodimers. Overall, our results show that the interaction between TMEM163 and distinct ZNT proteins is functionally relevant and that their heterodimerization may serve to influence their zinc efflux activity within specific tissues or cell types. Research HighlightsO_LITMEM163 protein heterodimerizes with mammalian ZNT1, ZNT2, ZNT3 and ZNT4 zinc efflux transporters. C_LIO_LITMEM163 and ZNT proteins partially co-localize in their respective plasma membrane or subcellular compartments, suggesting distinct cellular roles as homodimers and heterodimers. C_LIO_LIThe zinc efflux activity of TMEM163 or ZNT protein homodimers did not markedly differ from their TMEM163/ZNT heterodimer counterparts. C_LIO_LIFunctional TMEM163/ZNT heterodimers give further credence to the role of TMEM163 as a bona fide member of the SLC30 protein family C_LI

cell biology↗

bioRxiv2021

A comprehensive series of temporal transcription factors in the fly visual system

The brain consists of thousands of different neuronal types that are generated through multiple divisions of neuronal stem cells. These stem cells have the capacity to generate different neuronal types at different stages of their development. In Drosophila, this temporal patterning is driven by the successive expression of temporal transcription factors (tTFs). While a number of tTFs are known in different animals and across various parts of the nervous system, these have been mostly identified by informed guesses and antibody availability. We used single-cell mRNA sequencing to identify the complete series of tTFs that specify most Drosophila medulla neurons in the optic lobe. We tested the genetic interactions among these tTFs. While we verify the general principle that tTFs regulate the progression of the series by activating the next tTFs in the series and repressing the previous ones, we also identify more complex regulations. Two of the tTFs, Eyeless and Dichaete, act as hubs integrating the input of several upstream tTFs before allowing the series to progress and in turn regulating the expression of several downstream tTFs. Moreover, we show that tTFs not only specify neuronal identity by controlling the expression of cell type-specific genes. Finally, we describe the very first steps of neuronal differentiation and find that terminal differentiation genes, such as neurotransmitter-related genes, are present as transcripts, but not as proteins, in immature larval neurons days before they are being used in functioning neurons; we show that these mechanisms are conserved in humans. Our results offer a comprehensive description of a temporal series of tTFs in a neuronal system, offering mechanistic insights into the regulation of the progression of the series and the regulation of neuronal diversity. This represents a proof-of-principle for the use of single-cell mRNA sequencing for the comparison of temporal patterning across phyla that can lead to an understanding of how the human brain develops and how it has evolved.

developmental biology↗

bioRxiv2021

Restoration of DNA Integrity and Cell Cycle by Electric Stimulation in Planarian Tissues Damaged by Ionizing Radiation

Exposure to high levels of ionizing {gamma}-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally {gamma}-irradiated tissues of the planarian flatworm Schmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+ stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse damaging effects of high dose {gamma}-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.

developmental biology↗

bioRxiv2020

Challenges in Undergraduate Synthetic Biology Training: Insights from a Canadian iGEM Student Perspective

The last two decades have seen vigorous activity in synthetic biology research and ever-increasing applications of synthetic biology technologies. However, pedagogical research on synthetic biology is scarce, especially when compared to some scientific and engineering disciplines. Within Canada, there are only three universities that formally teach synthetic biology programs; two of which are at the undergraduate level. Many Canadian undergraduate students are instead introduced to synthetic biology through participation in the annual International Genetically Engineered Machine (iGEM) competition where they work in design teams to conceive of and execute a synthetic biology project that they present at an international jamboree. We surveyed the Canadian landscape of synthetic biology education through the experience of students from the Canadian iGEM teams of 2019. Using a thematic codebook analysis, we gathered insights to generate recommendations that could empower future iGEM team operations and inform educators about best practices in teaching undergraduate synthetic biology.

scientific communication and education↗