Biology subjects

Lee, D.

Publications and source records attributed to Lee, D..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Molecular and Epigenetic Pathways Underlying Epithelial Damage and Repair in Necrotizing Enterocolitis via Multi-omics Approach

IntroductionNeonatal necrotizing enterocolitis (NEC) is a severe gastrointestinal disorder with high mortality, characterized by epithelial cell injury and compromised epithelial repair. The mechanisms underlying defective epithelial regeneration remain poorly understood despite advances in single-cell omics. Addressing these challenges is essential for elucidating the pathogenesis of NEC and identifying therapeutic targets to restore epithelial regeneration and replace the damaged epithelial layer. MethodsMulti-omics approaches were employed to investigate molecular and spatial changes in experimental NEC at epigenetic and transcriptomic levels. These included bulk RNA sequencing, single-nucleus RNA sequencing (snRNA-seq), single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), and multiplexed error-robust fluorescence in situ hybridization (MERFISH) for spatial transcriptomics. Complementary in vitro experiments and in vivo mouse models were utilized to evaluate NEC phenotypes, intestinal tissue morphology, and organoid formation. ResultsChanges in cell type composition, transcriptional network remodeling, and chromatin accessibility were observed in the small intestine of neonatal mice with NEC. Chromatin accessibility significantly changed in epithelial cells, highlighting their pivotal roles in NEC. A marked reduction in intestinal stem cells (ISCs) and transit-amplifying cells, along with an increased proportion of enteroendocrine cells, indicates disrupted epithelial regeneration and functional differentiation. These changes correlated with disrupted WNT signaling and stem cell maintenance genes (e.g., Lgr5, Smoc2, Axin2) and activation of inflammatory and hypoxia-related pathways (e.g., Il6, Tnf). The epigenetic regulator Ezh2 was identified as a critical factor in maintaining LGR5+ ISCs and epithelial homeostasis. Knockdown of Ezh2 reduced stemness and proliferation-related gene expression and exacerbated inflammation. Reactivation of WNT signaling restored Ezh2 and Lgr5 expression, improving intestinal regeneration. ConclusionThis study reveals dynamic transcriptomic, epigenetic, and spatial changes in NEC and highlights Ezh2 as a key regulator of LGR5+ intestinal stem cell function and epithelial regeneration. These findings provide insights into NEC pathogenesis and a basis for therapies targeting Ezh2 and WNT signaling to restore intestinal integrity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/647851v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1ad89eaorg.highwire.dtl.DTLVardef@396282org.highwire.dtl.DTLVardef@172596forg.highwire.dtl.DTLVardef@4daf28_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

N1 cassette-lacking NMDA receptors mediate the antidepressant activity of ketamine

Ketamine has emerged as a rapid-acting and robust antidepressant1,2. However, the mechanism of its antidepressant action remains enigmatic. The core issue that has yet to be resolved is whether NMDA receptors (NMDARs), which are subject to open channel blockade by ketamine3,4, mediate the antidepressant effect. NMDARs naturally undergo alternative splicing of the obligatory GluN1 subunit5, producing receptor diversity in the brain that has not been considered in the actions of ketamine. Here we discover that alternative splicing of Grin1 exon 5, which leads to exclusion (GluN1a) or inclusion (GluN1b) of the N1 cassette, located in the N-terminal domain of GluN1 distant from the pore, unexpectedly dictates the level and dynamics of NMDAR blockade by ketamine and gates its antidepressant activity. We find that ketamine prevents NMDAR-dependent long-term potentiation (LTP) in the CA1 region of the hippocampus in mice engineered to exclude Grin1 exon 5 (GluN1a mice), but ketamine has no effect on LTP in mice engineered to include this exon (GluN1b mice). Ketamine inhibits synaptic NMDARs in CA1 pyramidal neurons in both GluN1a and GluN1b mice, with the level of steady-state blockade marginally greater in GluN1a- than in GluN1b-containing NMDARs. However, the rate of relief of ketamine blockade upon membrane depolarization is markedly slower in GluN1a than in GluN1b neurons such that GluN1a-containing receptors remain blocked during bursting activity, whereas those containing GluN1b escape the ketamine blockade. Furthermore, ketamine treatment, either via systemic administration or local infusion into the hippocampus, induces an antidepressant effect in GluN1a mice but has no effect in GluN1b mice. Collectively, we identify GluN1a-containing NMDARs, which are persistently blocked by ketamine during neuronal firing activity, to be selectively responsible for the antidepressant effect.

neuroscience↗

bioRxiv2025

Acetate metabolism during xylose fermentation enhances 3-hydroxypropionic acid production in engineered acid-tolerant Issatchenkia orientalis

Efficient bioconversion of acetate-rich lignocellulosic biomass into value-added chemicals remains a major challenge due to the toxicity of acetic acid. In this study, we engineered an acid-tolerant Issatchenkia orientalis strain (IoDY01H) capable of producing 3-hydroxypropionic acid (3-HP), a key bioplastic precursor, from glucose, xylose, and acetate. Using a Cas9-based genome editing system with a hygromycin B resistance marker, we introduced heterologous genes encoding xylose utilization and {beta}-alanine-based 3-HP biosynthetic pathways into the I. orientalis genome. Metabolomic analysis revealed that acetate supplementation redirected metabolic flux toward amino acid and lipid metabolism while reducing TCA cycle intermediates. Acetate enhanced 3-HP production by promoting accumulation of {beta}-alanine, but also revealed {beta}-alanine-pyruvate aminotransferase as a metabolic bottleneck under acidic conditions. Using pretreated hemp stalk hydrolysate as a feedstock, the engineered strain achieved a 3-HP titer of 8.7 g/L via separate hydrolysis and fermentation (SHF), outperforming simultaneous saccharification and fermentation (SSF). These findings demonstrate the feasibility of producing 3-HP from acetate-rich biomass using engineered non-conventional yeast and highlight I. orientalis as a promising microbial chassis for industrial bioconversion. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/649204v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@c04442org.highwire.dtl.DTLVardef@c16b4aorg.highwire.dtl.DTLVardef@6af6d9org.highwire.dtl.DTLVardef@743029_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIEngineered I. orientalis co-utilized xylose and acetate to produce 3-HP. C_LIO_LIAcetate addition enhanced 3-HP production during xylose fermentation. C_LIO_LIAcetate redirected metabolic flux toward 3-HP biosynthesis pathways. C_LIO_LIEngineered I. orientalis achieved 8.7 g/L 3-HP from hemp stalk hydrolysate via SHF. C_LI

synthetic biology↗

bioRxiv2025

Designed NGF mimetics with reduced nociceptive signatures in neurons

The clinical use of Nerve Growth Factor (NGF) for neuronal regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75NTR; pain sensitization is thought to involve p75NTR. We sought to overcome this limitation by de novo design of a TrkA agonist that does not bind p75NTR. We designed homodimeric TrkA engaging constructs that dimerize TrkA subunits in a variety of geometries, and identified those eliciting the strongest signaling. The resulting designed agonists are able to stimulate transdifferentiated neurons and neuroblastoma cell lines, leading to neurite outgrowth and neuronal differentiation, with considerably reduced transcription of inflammation and pain related genes. These agonists are promising candidates for promoting neuronal regeneration without adverse side effects. HighlightsO_LIDe novo designed TrkA agonists activate MAPK and PI3K-AKT signaling C_LIO_LIRigid fusions allow for highly tunable signaling signatures C_LIO_LITrkA agonists lead to neurite outgrowth in neuroblastoma cells comparable to retinoic acid C_LIO_LIModulation of the TrkA pathway without co-stimulating p75NTR leads to a downregulation of inflammatory and nociceptive signature in neurons. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/648806v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@c48066org.highwire.dtl.DTLVardef@c9c5a7org.highwire.dtl.DTLVardef@cf8ebdorg.highwire.dtl.DTLVardef@a4345a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Implementation of an adaptive-optics assisted isoSTED nanoscope

The highest level of three-dimensional (3D) resolution in stimulated emission depletion (STED) nanoscopy involves harnessing a 4Pi architecture using two opposing objectives. This protocol describes the construction and alignment of a 4Pi-STED nanoscope, commonly referred to as an isoSTED nanoscope. It guides interested researchers through assembling optomechanical components, configuring electronic and control devices, aligning the optical beam path, and assessing the instruments performance. Designed for adept optical instrument builders, this protocol offers a detailed roadmap for constructing an isoSTED nanoscope with adaptive optics (AO) in approximately 12 months. With this finely calibrated instrument, researchers can achieve 3D biological images with isotropic sub-50-nm resolution in thick samples up to 35 {micro}m in depth.

bioengineering↗

bioRxiv2025

Strain-specific differences in toxT expression and virulence gene activation in Vibrio cholerae

The transcriptional activator ToxT is a key regulator of Vibrio cholerae virulence, controlling the expression of cholera toxin (CT) and the toxin co-regulated pilus (TCP). Insights into the regulation and function of toxT have largely come from studies on the classical biotype strain O395, which exhibits robust toxT expression. However, toxT expression is not fully consistent across V. cholerae strains. Here, we show that toxT transcription and protein production differ significantly among strains, particularly in El Tor biotype, which exhibit allele-dependent regulatory constraints. Using qRT-PCR and Western blotting, we demonstrate that alternative toxT alleles confer distinct transcriptional activator functions across El Tor biotype strains. Notably, IB5230, a pandemic El Tor strain, exhibits enhanced toxT and virulence gene expression even at 37{degrees}C, suggesting a potential adaptation for increased pathogenicity. Our results suggest that toxT autoregulatory feedback plays a more critical role in virulence gene activation than previously recognized. This study underscores previously unrecognized complexity in toxT regulation, emphasizing the need to reassess virulence control mechanisms in epidemic and emerging V. cholerae strains. Understanding these strain-specific differences is essential for refining models of cholera pathogenesis. Author SummaryCholera is a severe diarrheal disease caused by the bacterium Vibrio cholerae, which continues to pose a major threat to global health. The ability of V. cholerae to cause disease depends on the expression of two key virulence factors--cholera toxin (CT) and the toxin-coregulated pilus(TCP)-- controlled by the transcriptional activator ToxT. While much of our understanding of ToxT regulation is based on classical biotype strains, most recent cholera outbreaks have been driven by El Tor biotype strains. In this study, we demonstrate that toxT expression and its ability to activate virulence genes vary markedly across V. cholerae strains, depending on both the specific toxT allele and the genetic background. Using isogenic strains engineered to express different toxT alleles, we show that some alleles are transcriptionally silent in certain El Tor strains while others are active, despite having similar functional capabilities when expressed. Notably, a hypervirulent strain linked to the Haitian cholera outbreak maintained high toxT expression even at human body temperature, hinting at possible adaptive mechanisms for enhanced pathogenicity. Our findings suggest that virulence regulation in V. cholerae may be more variable than previously recognized, highlighting strain- and allele-specific differences in toxT expression. Understanding these strain- and allele-specific differences in virulence gene regulation is crucial for improving models of cholera pathogenesis and could inform the development of more effective interventions and vaccines against this evolving pathogen.

microbiology↗

bioRxiv2025

Temporal and Spatial Scales of Resting-state Human Cortical Activity Throughout Lifespan

Sensorimotor and cognitive abilities undergo substantial changes throughout the human lifespan, but the corresponding changes in the functional properties of cortical networks remain poorly understood. This can be studied using temporal and spatial scales of functional magnetic resonance imaging (fMRI) signals, which provide a robust description of the topological structure and temporal dynamics of neural activity. For example, timescales of resting-state fMRI signals parsimoniously predict a significant amount of the individual variability in functional connectivity networks identified in adult human brains. In the present study, we quantified and compared temporal and spatial scales in resting-state fMRI data collected from 2,352 subjects between the ages of 5 and 100 in Developmental, Young Adult, and Aging datasets from the Human Connectome Project. For most cortical regions, we found that both temporal and spatial scales decreased with age throughout the lifespan, with the visual cortex and the limbic network consistently showing the largest and smallest scales, respectively. For some prefrontal regions, however, these two scales displayed non-monotonic trajectories and peaked around the same time during adolescence and decreased throughout the rest of the lifespan. We also found that cortical myelination increased monotonically throughout the lifespan, and its rate of change was significantly correlated with the changes in both temporal and spatial scales across different cortical regions in adulthood. These findings suggest that temporal and spatial scales in fMRI signals, as well as cortical myelination, are closely coordinated during both development and aging. Significance StatementTemporal and spatial scales of resting-state cortical activity in humans measured by fMRI largely decreased throughout the lifespan, except that for some regions in the prefrontal cortex they peaked similarly during adolescence. In addition, whereas cortical myelination consistently increased throughout the lifespan, its variation across different cortical networks and the rate of age-related changes were correlated with the dynamics of temporal and spatial scales of rs-fMRI activity, suggesting that the spatio-temporal scales of cortical activity and cortical myelination might be co-regulated during development and aging.

neuroscience↗

bioRxiv2025

Molecular kinetics dictate population dynamics in CRISPR-based plasmid defense

Understanding and manipulating mobile genetic element (MGE) spread within bacterial communities represents a great challenge with wide-ranging potential benefits. It requires a detailed understanding of spatial effects and cell-to-cell variability in defence systems such as CRISPR-Cas. Here, we report a time-lapse imaging-based assay with simultaneous fluorescent labeling of CRISPR-Cascade complexes and the conjugative plasmid RP4, enabling direct, single-cell-resolution observation of conjugation and CRISPR interference. We find that Cascade, under wild-type-like expression scenarios, provides a nudge towards plasmid clearance rather than full immunity, and can be counteracted by the ParDE plasmid addiction system. These limitations could be overcome by higher Cascade expression, yet by quantifying single-cell variability, we observe a tradeoff between plasmid clearance and cell growth. We synthesize these measurements into a spatially-resolved, agent-based model of plasmid population dynamics. The imaging and analysis techniques used here will facilitate disentanglement of how single-cell molecular events result in community-wide plasmid dynamics.

molecular biology↗

bioRxiv2025

Gold Nanocages as Scattering Contrast Agents for Optical Coherence Tomography

We report a scattering-dominant agent that significantly enhances optical coherence tomography (OCT) imaging contrast. The agent is based on gold nanocages, which exhibit a surface plasmon resonance (SPR) peak around 780 nm and a scattering cross-section that exceeds the absorption cross-section. The synthesis protocol for these nanocages is provided in detail. The optical properties of the gold nanocages were characterized using OCT imaging and further validated with integrating sphere measurements. OCT contrast enhancement was demonstrated through imaging of tissue phantoms containing embedded nanocages, as well as ex vivo imaging of mouse tissues and in vivo imaging of a mouse tumor following intravenous administration of PEGylated gold nanocages. To the best of our knowledge, this may be the first demonstration of scattering-dominant OCT contrast agents utilizing structured gold nanoparticles.

bioengineering↗

bioRxiv2025

Gold Nanocages with a Long SPR Peak Wavelength as Contrast Agents for Optical Coherence Tomography Imaging at 1060 nm

There has been growing interest in optical coherence tomography (OCT) imaging at a wavelength of 1060 nm. However, potential contrast agents for OCT imaging at this specific wavelength has not been thoroughly investigated. In this study, we present the synthesis and optical characterization of gold nanocages with a small edge length ([~]65 nm) and a surface plasmon resonance peak around 1060 nm. These nanocages represent a class of potential contrast agents for OCT at 1060 nm. OCT imaging experiments were conducted on phantoms and in vivo mouse tissues using a 1060-nm swept-source OCT system, demonstrating significant enhancement in imaging contrast due to the presence of the gold nanocages. GRAPHICAL ABSTRACTGold nanocages with a long SPR peak wavelength as OCT imaging contrast agents at 1060 nm O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/642209v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@179a727org.highwire.dtl.DTLVardef@1cd1e4eorg.highwire.dtl.DTLVardef@180ce47org.highwire.dtl.DTLVardef@166a779_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Precise, Specific, and Sensitive De Novo Antibody Design Across Multiple Cases

The precision design of antibodies, which naturally recognize diverse molecules through six variable loops, remains a critical challenge in therapeutic molecule discovery. In this study, we demonstrate that precise, sensitive, and specific antibody design can be achieved without prior antibody information across eight distinct target proteins. For each target, binders were identified from a yeast display scFv library of approximately 106 sequences, constructed by combining 102 designed light chain sequences with 104 designed heavy chain sequences. Binders with varying binding strengths were identified for all eight targets, including a case where no experimentally resolved target protein structure was available, demonstrating the highest level of precision compared to previous de novo antibody design reports. To further validate the designed antibodies, they were characterized in the IgG format for five distinct targets. The antibodies exhibited favorable developability properties, positioning them as promising hit or lead candidates. Notably, for one target in particular, the IgG-formatted antibodies exhibited affinity, activity, and developability, comparable to a commercial antibody, highlighting the sensitivity of the design method. Furthermore, binders capable of distinguishing closely related protein subtypes or mutants were identified, demonstrating that the method can achieve high molecular specificity. Cryo-EM analysis experimentally validated the designs accuracy by confirming that the key binding interactions were precisely as designed. These findings underscore the effectiveness of precision molecular design based on atomic-accuracy structure prediction. This study establishes computational antibody design as a viable approach for generating therapeutic molecules with tailored properties, with promising potential for achieving the efficacy and safety required for successful therapeutics.

bioengineering↗

bioRxiv2025

Antibody-Free Immunopeptide Nano-Conjugates for Brain-Targeted Drug Delivery in Glioblastoma Multiforme

Glioblastoma Multiforme (GBM) represents a significant clinical challenge amongst central nervous system (CNS) tumors, with a dismal mean survival rate of less than 8 months, a statistic that has remained largely unchanged for decades (National Brain Society, 2022). The specialized intricate anatomical features of the brain, notably the blood-brain barrier (BBB), pose significant challenges to effective therapeutic interventions, limiting the potential reach of modern advancements in immunotherapy to impact these types of tumors. This study introduces an innovative, actively targeted immunotherapeutic nanoconjugate (P12/AP-2/NCs) designed to serve as an immunotherapeutic agent capable of traversing the BBB via LRP-1 receptor-mediated transcytosis. P12/AP-2/NCs exert its immune-modulating effects by inhibiting the PD-1/PD-L1 axis through a small-size PD-L1/ PD-L2 antagonist peptide Aurigene NP-12 (P12). P12/AP-2/NCs are synthesized from completely biodegradable, functionalized high molecular weight {beta}-poly(L-malic acid) (PMLA) polymer, conjugated with P12 and Angiopep-2 (AP2) to yield P12/AP-2/NCs. Evaluating nanoconjugates for BBB permeability and 3-D tumor model efficacy using an in vitro BBB-Transwell spheroid based model demonstrating successful crossing of the BBB and internalization in brain 3D tumor environments. In addition, the nanoconjugate mediated T cells cytotoxicity on 3D tumor region death in a U87 GBM 3-D spheroid model. AP2/P12/NCs is selectively inhibited in PD1/PDL1 interaction on T cells and tumor site, increasing inflammatory cytokine secretion and T cell proliferation. In an in-vivo murine brain environment, rhodamine fluorophore-labeled AP2/P12/NCs displayed significantly increased accumulation in the brain during 2-6 h time intervals post-injection with a prolonged bioavailability over unconjugated peptides. AP2/P12/NCs demonstrated a safety profile at both low and high doses based on major organ histopathology evaluations. Our findings introduce a novel, programmable nanoconjugate platform capable of penetrating the BBB for directed delivery of small peptides and significant immune environment modulation without utilizing antibodies, offering promise for treating challenging brain diseases like glioblastoma multiforme and beyond.

immunology↗

bioRxiv2025

Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci

Genome-wide association studies (GWAS) have identified >30 loci with multiple common noncoding variants explaining interindividual electrocardiographic QT interval (QTi) variation. Of the many types of noncoding functional elements, here we sought to identify transcriptional enhancers with sequence variation and their cognate transcription factors (TFs) that alter the expression of proximal cardiac genes to affect QTi variation. We used massively parallel reporter assays (MPRA) in mouse cardiomyocyte HL-1 cells to screen for functional enhancer variants among 1,018 QTi-associated GWAS variants that overlap candidate cardiac enhancers across 31 loci. We identified 445 GWAS variant-containing enhancers of which 79 showed significant allelic difference in enhancer activity across 21 GWAS loci, with multiple enhancer variants per locus. Of these, we predicted differential binding by cardiac TFs, including AP-1, ATF-1, GATA2, MEF2, NKX2.5, SRF and TBX5 which are known to play key roles in development and homeostasis, at 49 enhancer variants. Finally, we used expression quantitative trait locus mapping and predicted promoter-enhancer contacts to identify 14 candidate target genes through analyses of 36 enhancer variants at 16 loci. This study provides strong evidence for 14 cardiac genes, 10 of them novel, impacting on QTi variation, beyond explaining observed genetic associations.

genetics↗

bioRxiv2025

Clinico-genomic features predict distinct metastatic phenotypes in cutaneous melanoma

Metastasis drives mortality and morbidity in cancer. While some patients develop broad metastatic disease across multiple organs, others exhibit organ-specific spread. To identify mechanisms underlying metastatic organotropism, we analyzed clinico-genomic data from over 7,000 patients with metastatic cutaneous melanoma in three independent cohorts (one primary discovery and two validation cohorts including a nationwide electronic health record-derived deidentified database), leveraging machine learning approaches to clinical data. We found that female sex and increased tumor mutational burden associate with decreased metastatic potential, while older age associates with increased lung and adrenal metastases. Using unsupervised analyses, patients clustered into five metastatic patterns: a "highly metastatic" cluster characterized by involvement of many organs, a "low metastatic" cluster characterized by few metastatic sites (mostly lymph node metastases), and three additional clusters each characterized by metastasis to specific sites (brain, lung, liver). Mutations in B2M and PTEN associated with increased overall metastatic potential. PTEN mutations were also associated with brain metastases but were enriched only in the "highly metastatic" cluster and not the brain-specific cluster. Mutations in GNAQ or GNA11 (GNA) associated with increased liver metastasis. To validate this association, we tested and demonstrated liver tropism in two GNA-mutant genetically engineered cutaneous melanoma mouse models of metastasis. Overall, our study elucidates distinct phenotypes of metastasis in patients with melanoma and identifies novel clinical and genomic associations that illuminate the drivers of clinical metastatic organotropism.

cancer biology↗

bioRxiv2025

The Binary Cellular Biology of Human Growth I Quantifying the Creation and Growth of the Body and its Parts

Assessing and understanding the Growth and Development of animals generally, and of human fetuses specifically, provides essential information for the management of the health of the newborn and its mother. Here we show that a consideration of the formation of the body, in units of numbers of cells, N, and the change in these numbers by the binary either/or decisions of cells to divide or not, an approach we call Binary Cellular Analysis, provides new insights and new equations for quantifying the growth and development of the body and its parts. These equations include: 1) The Binary Cellular Universal Growth Equation, which captures growth from conception to adulthood, and provides a method for biologically-based, data-driven, Growth Curves; 2) The Binary Cellular Universal Mitotic Fraction Equation, which lies within the Binary Cellular Universal Growth Equation, and captures the mechanism of growth to adult size, control of cell division; 3) The Binary Cellular Allometric Growth Equation, which captures the creation and growth of the Tissues, Organs, and Anatomical Structures of the body, and how the embryo creates each Body Part from a Single Founder Cell; and, 4) Binary Cellular Estimated Fetal Weight Equations, derived from the Binary Cellular Allometric Growth Equation, which captures the relationship between Ultrasound Measurement and the Size of the body as a whole. These equations capture the developmental process of Cellular Selection, resulting from Differential Cellular Proliferation, which molds the formation of the body from a single fertilized ovum into a multicellular animal. The parameters of these equations both capture the differences in Size and Growth between animals across the taxonomic spectrum, and between human fetuses, as well as identify the individual mechanisms of mitosis that drive Growth and Development. From the Binary Cellular Universal Growth Equation, the Growth of human fetuses can be measured, thus providing a much-needed tool for understanding the biological forces that cause a fetus to grow to Small, Average, or Large Size at birth, for providing the basis of biologically-based, data-driven, Growth Curves, and for assisting the management of the obstetric care of the fetus and its mother.

developmental biology↗

bioRxiv2025

Multilayer regulation underlies the functional precision and evolvability of the olfactory system

Sensory neurons must be reproducibly specified to permit accurate neural representation of external signals but also able to change during evolution. We studied this paradox in the Drosophila olfactory system by establishing a single-cell transcriptomic atlas of all developing antennal sensory lineages, including latent neural populations that normally undergo programmed cell death (PCD). This atlas reveals that transcriptional control is robust, but imperfect, in defining selective sensory receptor expression. A second layer of precision is afforded by the intersection of expression of functionally-interacting receptor subunits. A third layer is defined by stereotyped PCD patterning, which masks promiscuous receptor expression in neurons fated to die and removes "empty" neurons lacking receptors. Like receptor choice, PCD is under lineage-specific transcriptional control; promiscuity in this regulation leads to previously-unappreciated heterogeneity in neuronal numbers. Thus functional precision in the mature olfactory system belies developmental noise that might facilitate the evolution of sensory pathways.

developmental biology↗

bioRxiv2025

Keystone engineering enables collective range expansion in microbial communities

Keystone engineers profoundly influence microbial communities by altering their shared environment, often by modifying key resources. Here, we show that in an antibiotic-treated microbial community, bacterial spread is controlled by keystone engineering affecting dispersal--an effect hidden in well-mixed environments. Focusing on two pathogens, non-motile Klebsiella pneumoniae and motile Pseudomonas aeruginosa, we found that both tolerate a {beta}-lactam antibiotic, with Pseudomonas being more resilient and dominating in well-mixed cultures. During range expansion, however, the antibiotic inhibits Pseudomonas ability to spread unless it is near Klebsiella--Klebsiella degrades the antibiotic to create a "clear zone" that allows Pseudomonas to expand, at the expense of Klebsiellas own growth, thus acting as a keystone engineer. As Pseudomonas spreads, it competitively suppresses Klebsiella. Our modeling and experimental analyses reveal that this keystone effect operates at a millimeter scale. We also observed similar keystone engineering by a Bacillus species isolated from a hospital sink, in both pairwise and eight-member bacterial communities with its co-isolates. These findings suggest that spatially explicit experiments are essential to understand certain keystone engineering mechanisms and have implications for surface-associated microbial communities like biofilms, as well as for diagnosing and treating polymicrobial infections involving drug-degrading, non-motile (e.g., Klebsiella), and drug-tolerant, motile (e.g., Pseudomonas) bacteria.

ecology↗

bioRxiv2024

Transcriptional Regulation of Neuropeptide Receptors Decodes Complexity of Peptidergic Modulation of Behavior and Physiology.

The modulation of complex behaviors in response to environmental and physiological contexts is a fundamental aspect of animal biology, with neuropeptides (NPs) playing a crucial role in this process. This study investigates the transcriptional regulation of neuropeptide receptors (NPRs) as a mechanism for context-dependent neuropeptidergic modulation of physiology and behavior. We hypothesize that the transcriptional control of NPR genes, rather than the NPs themselves, is a critical determinant in the context-dependent modulation of behavior and physiology. Using a multi-faceted approach, including comparative genomics, transcription factor network analysis, and empirical validation in model organisms such as Drosophila melanogaster, we reveal a complex regulatory landscape where NPR expression is tightly controlled. Our findings demonstrate that NPR genes exhibit a higher number of enhancers, CTCF-binding sites, and open chromatin regions compared to NP genes, suggesting a greater susceptibility to transcriptional modulation. This regulatory architecture allows for precise control over neuropeptidergic signaling, enabling dynamic and context-specific behavioral and physiological responses. Our results highlight the importance of NPR-expressing cells by transcriptional regulation in mediating the effects of NPs on behavior and physiology. We show that this regulation is conserved across species, indicating an evolutionarily significant mechanism for fine-tuning neuropeptidergic signaling. Furthermore, our study provides insights into the distinct regulatory mechanisms underlying the multifunctionality of NPs and their receptors, offering a novel perspective on the transcriptional control of complex behaviors. In conclusion, this study advances our understanding of neuropeptidergic signaling by focusing on the transcriptional regulation of NPRs. Our findings have broad implications for the development of therapeutic strategies targeting neuropeptidergic systems in various neurological and behavioral disorders.

neuroscience↗