Biology subjects

Gonzalez, J. E.

Publications and source records attributed to Gonzalez, J. E..

5 recordsLinked to original sources

bioRxiv2026

Exhaustive Isotope Tracing Reveals the Butterfly Effect of Mammalian Producer Cell Line Selection for Biomanufacturing

Chinese hamster ovary (CHO) cells are the dominant platform for recombinant biotherapeutics, yet the impact of producer cell line selection on mammalian cell metabolism remains poorly understood. Here, we performed 41 independent 13C-tracer experiments using uniformly labeled glucose or individual amino acids to comprehensively map carbon utilization in the two principal CHO production platforms: methotrexate-selected CHO-K1 and glutamine synthetase-selected CHO-GS cells. Time-resolved GC-MS analysis revealed distinct metabolic phenotypes spanning central carbon metabolism, amino acid interconversion, lipid biosynthesis, and one-carbon metabolism. CHO-K1 cells exhibited extensive reductive carboxylation and pyruvate carboxylase-mediated anaplerosis, whereas CHO-GS cells redirected glutamate toward glutamine synthesis and relied on asparagine and aspartate to support TCA cycle activity. Isotopomer analysis uncovered substantial intracellular-extracellular cycling of alanine, glycine, glutamate, and serine despite contrasting uptake profiles and quantified differential amino acid contributions to fatty acids and cholesterol. Serine, glycine, and methionine labeling revealed active folate-cycle interconversion in CHO-K1 and enhanced methionine-cycle activity in CHO-GS. Aspartate is identified as a key redox exchange factor and uniquely informative tracer for pathway characterization following glutamine depletion. Together, this exhaustive isotope-tracing framework establishes how producer cell line selection rewires mammalian metabolism and provides a foundation for cell engineering, media optimization, metabolic modeling, and next-generation biomanufacturing.

cell biology↗

bioRxiv2026

Time space signatures of hybrid search resolution using EEG and eye movements concurrent recordings

Understanding how the brain supports visual search in naturalistic environments--where attention and memory must work together to find targets among distractors--requires analysing neural signals where responses overlap in time and multiple environmental variables simultaneously interact. Conventional event-related methods cannot disentangle these overlapping signals, creating a fundamental bottleneck for studying cognition in ecologically valid settings. Here, we seek to isolate activation patterns during a hybrid visual and memory search task in naturalistic scenarios. We show that our deconvolution-based approach applied to coregistered EEG and eye-tracking data resolves this problem, capturing fine-grained activation patterns in the temporal response functions (TRFs) for main effects and their interactions. Starting from hypothesis-driven models, we replicated established components for visual processing and target detection in a Hybrid Search task with unrestricted eye movements. Moreover, extending our approach to hierarchically larger data-driven models enabled us to explore interactions between the effects that have otherwise been studied separately. We showed that the TRF estimates remained stable with increasing model complexity, supported by improved model performance (Pearsons correlation coefficient) and controlled by the variance inflation factor (VIF). We identified a late activation consistent with the P300 component for target detection, and revealed that missed detections elicited similar but weaker responses, suggesting a more nuanced role than simple detection. These findings demonstrate how deconvolution methods, complemented with robust measures of model performance that support its expansion in features space, can uncover the dynamic interplay of attention and memory processes underlying free-viewing behavior.

neuroscience↗

bioRxiv2026

Exposure to the antimicrobial peptides LL-37 and ATRA-1 induces a lipidome response in Staphylococcus aureus that alters membrane biophysical properties

Staphylococcus aureus (S. aureus) is an opportunistic pathogen that is a global health concern for its ability to cause a wide spectrum of clinical infections. Due to the emergence of resistance to commonly used antibiotics, there has been interest in exploring the use of antimicrobial peptides to treat S. aureus infections. However, changes in the lipid composition of the lipid bilayer membrane can alter the activity of peptides, and S. aureus is able to induce variations in lipid composition in response to environmental stress. Here, we explore how the main lipid components in S. aureus are altered when exposed to LL-37, a human cathelicidin involved in primary immune response, and ATRA-1, a short antimicrobial peptide derived from the snake Naja atra venom. A lipidomic study is conducted through HPLC-MS-MS (LC-ESI-MS/MS) to quantify phosphatidylglycerol, cardiolipin, lysyl-phosphatidylglycerol, monogalacto- and digalacto-diacylglycerol, and carotenoids. In addition, menaquinones, responsible for electron transport during oxidative phosphorylation, were also quantified. Biophysical properties such as membrane electric surface potential and lipid packing were assessed. We find that lipid adaptation is specific to the type of antimicrobial peptide, where ATRA-1 mainly induces changes in the electric surface potential through variations in Lysyl-PG, while exposure to LL-37 changes carotenoid levels, inducing an increase in membrane rigidity as measured by FTIR. In addition, both peptides induce a reduction in menaquinone and DGDG levels. These findings highlight the role of membrane lipid remodeling as a peptide-specific response mechanism in S. aureus, with implications for the development of AMP-based therapies. HighlightsO_LIStaphylococcus aureus responds through shifts in lipid composition and membrane biophysical properties to exposure to the antimicrobial peptides LL-37 and ATRA-1. C_LIO_LIBoth LL-37 and ATRA-1 lead to shifts in the glycolipids MGDG and DGDG; two lipids involved in regulating negative membrane curvature stress and responsible for shifting resistance to antimicrobial peptide activity in Staphylococcus aureus. C_LIO_LILL-37 treatment leads to an overall reduction in carotenoid content in Staphylococcus aureus, including the carotenoid end-product staphyloxanthin and the precursor 4,4-diaponeurosporenoic acid. Both lipids regulate membrane biophysical properties and protect Staphylococcus aureus from oxidative stress. C_LIO_LIBoth LL-37 and ATRA-1 lead to a reduction in menaquinone levels, which are involved in the electron transport chain during oxidative phosphorylation. Reduction in these menaquinones have been associated to the formation of small colony variants that are often observed in chronic Staphylococcus aureus infections. C_LI

biophysics↗

bioRxiv2025

Mapping neural activity during naturalistic visual and memory search

In everyday life, individuals often search for one of several items stored in memory. This cognitive process, known as hybrid search, is critical for tasks like navigating using landmarks. While the behavioral aspects of hybrid search have been extensively studied, the underlying neural mechanisms remain less understood. In this study, we combined concurrent magnetoencephalography (MEG) and eye movement recordings to investigate the oscillatory and evoked neural dynamics supporting hybrid search in naturalistic settings. Twenty-one participants (12 males, 9 females) performed a free-viewing task involving visual search for targets embedded in memory (hybrid search) across naturalistic scenes. Time-Frequency analyses revealed specific neural signatures during memory encoding, retention, and visual search. During encoding and retention, posterior alpha-band power decreased with memory load, reflecting heightened perceptual and mnemonic demands. During visual search, frontoparietal beta-band activity scaled with memory load, suggesting increased cognitive control. By aligning MEG signals to eye movement events and applying source reconstruction, we identified an early visually evoked lambda response, localized to V1, followed by a distributed P3m component, with maximum activation in the right inferior parietal lobe, that discriminated target from distractor fixations. Together, these findings demonstrate how oscillatory and evoked responses dynamically support hybrid search in naturalistic settings, revealing how memory, attention, and visual processing interact during active vision. Significance statementUnderstanding how the brain supports everyday tasks, like searching for familiar objects, requires studying cognition under realistic conditions, yet most knowledge comes from highly controlled lab tasks with simple stimuli. Here, we combined MEG and eye-tracking to examine how the brain supports free-viewing hybrid search -looking for any of several remembered items-across natural scenes. We found memory load modulations in posterior alpha oscillations during encoding and retention, as well as in frontoparietal beta oscillations during search. By time-locking neural signals to eye movements, we identified a robust marker of target detection. These findings provide direct evidence of how attention, memory, and vision interact in realistic settings, helping bridge the gap between controlled experimental paradigms and real-world cognition.

neuroscience↗

bioRxiv2018

A Novel Denitrification Regulator, Adr, Mediates Denitrification Under Aerobic Conditions in Sinorhizobium meliloti

Sinorhizobium meliloti is a soil dwelling bacteria capable of forming a symbiotic relationship with several legume hosts. Once symbiosis is established, S. meliloti fixes atmospheric nitrogen into nitrogenated compounds, thus carrying out an important step in the nitrogen cycle. S. meliloti is also capable of the reverse process, denitrification, the reduction of nitrate and nitrite to nitrogen gas. In this study we have identified a novel regulator of denitrification in S. meliloti, Adr, which affects the expression of the denitrification genes in aerobically grown cultures. Analysis of the Adr sequence reveals a LuxR-like quorum sensing regulator, however, it does not respond to the known quorum sensing signals produced by S. meliloti. Additionally, we show that FixJ, the major regulator of denitrification and microaerobic respiration in S. meliloti, is active under our growth conditions. Comparison of the FixJ microarray to our Adr microarray shows a significant overlap between the two regulons. We also show that while Adr is not necessary for symbiotic nitrogen fixation, a functional copy of this regulator confers a competitive advantage to S. meliloti during host invasion. Our findings suggest that Adr is a new type of denitrification regulator and that it acts at the same regulatory level as FixJ.\n\nImportanceRhizobia contribute to the nitrogen cycle by fixing atmospheric nitrogen to nitrogenated compounds and by denitrification, the reduction nitrate and nitrite to nitrogen gas. Denitrification enhances the survival of Sinorhizobium meliloti in the various environments it may encounter, such as free-living conditions in the rhizosphere, during invasion of the plant host, and after a symbiotic relationship has been established. Oxygen concentration is the typical signal for denitrification gene expression. Recent studies of low oxygen cultures of S. meliloti have outlined the regulation structure for denitrification. In this study, we examine the regulation of denitrification in aerobically grown S. meliloti cultures. Understanding how S. meliloti responds to various oxygen concentrations will result in a more complete picture of denitrification regulation in this agriculturally important organism and the impact of denitrification on the soil microbiome as a whole.

microbiology↗