Biology subjects

Connolly, L.

Publications and source records attributed to Connolly, L..

5 recordsLinked to original sources

bioRxiv2026

Domestication, spread, and improvement have shaped biological nitrogen fixation traits in Zea taxa

Synthetic nitrogen fertilizers enhance maize (Zea mays ssp. mays) productivity but impose substantial environmental and economic costs. Some Mexican maize landraces support biological nitrogen fixation (BNF) in aerial root mucilage, raising the question of how much variation exists in this trait and how domestication, geographic spread, and improvement have shaped BNF-related traits across Zea in the Americas. We evaluated aerial root traits and BNF capacity across the maize domestication continuum using 60 Zea accessions grown in field experiments over two years under low-N conditions. Some accessions of wild Zea, landraces from Mexico and South America, and improved varieties had elevated nitrogen derived from the atmosphere (%Ndfa), ranging from 20 to 40%; some of these also had greater %Ndfa than typical improved varieties. Spread and improvement appear to have significantly reduced the number of aerial root-bearing nodes, with wild Zea and Mexican landraces consistently producing more. Nevertheless, the proportion of nitrogen derived from the atmosphere (%Ndfa) does not vary systematically across the domestication continuum. Thus, crop evolution shaped aerial root phenotypes more than associative BNF capacity. The persistence of substantial within-group variation indicates that the genetic potential for enhanced BNF remains within the Zea gene pool, providing opportunities to encourage and improve nitrogen use efficiency in maize cropping systems.

ecology↗

bioRxiv2026

N-Terminal Alkylation of Proteins with Triazole-4-carbaldehyde for Targeted Liposome Engineering

A platform method to associate native proteins and peptides onto a liposome membrane using site-specific N-terminal alkylation based on 1H-1,2,3-triazole-4-carbaldehyde (TA4C) is developed. The TA4C reagent reacts with the N-terminal -amino group of native proteins under mild aqueous conditions in a single step, without genetic engineering or protecting group strategies. Equipping TA4C with hexyl and nonyl chains provides a direct handle for tuning the association between the protein and membrane. N-terminal alkylation of green fluorescent protein (GFP) as a model proceeds in high yield (93% for the hexyl group and 70% for the nonyl group), and tethering the N-terminal alkyl group on GFP efficiently associates the protein with the liposomal membrane, as confirmed by confocal laser scanning microscopy and dynamic light scattering. We extended this strategy to an investigation of the GE11 peptide, a ligand for the epidermal growth factor receptor (EGFR). The liposome immobilized with GE11 peptide possessing an N-terminal alkyl group enables active targeting with EGFR-overexpressing A431 cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/742023v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@9c5ec3org.highwire.dtl.DTLVardef@117765org.highwire.dtl.DTLVardef@b5c471org.highwire.dtl.DTLVardef@1741293_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Hyaluronic Acid and Emergent Tissue Mechanics Orchestrate Digit Tip Regeneration

Tissue regeneration is a dynamic process requiring coordinated cell fate decisions to restore structure and function. For instance, the tips of human and rodent digits fully regrow after amputation, although more proximal injuries fail to regenerate. While biochemical cues have been widely studied in wound healing, the role of the physical microenvironment remains less understood. Here, we discovered that tissue mechanics and extracellular matrix (ECM) composition differ markedly between non-regenerating and regenerating wounds. These differences are due to specific fibroblast sub-types which predominate in the non-regenerating wound and form fibrotic collagen networks. Conversely, bone-forming progenitors in regenerating digits synthesize abundant hyaluronic acid, which mediates collagen fibrillogenesis. By modeling the tissue mechanics of non-regenerative and regenerative wounds using hydrogels, we showed that substrate stiffness regulates the synthesis of fibrotic and regenerative ECM. We further revealed that mimicking the regenerative wound mechanics upregulated bone morphogenic protein signaling and osteogenic differentiation. We ultimately demonstrated that the link protein HAPLN1 promotes hyaluronic acid deposition in vivo, reduces scar formation, and induces bone repair after non-regenerative amputations. These findings emphasize the interplay among the ECM, tissue mechanics, and cell behavior in digit regeneration and point towards ECM modulation as a strategy to improve wound healing. HighlightsO_LINon-regenerating and regenerating digit tips diverge in their cellular and ECM composition C_LIO_LIRegeneration requires hyaluronic acid matrix, which mediates collagen assembly and tissue mechanics C_LIO_LISoft substrates enhance BMP signaling and propagate the synthesis of regenerative ECM C_LIO_LIHAPLN1 overexpression initiates rescue of non-regenerative digit tip amputations C_LI

developmental biology↗

bioRxiv2024

Structural and Dynamical Analyses of Apo and Cap-binding eIF4E: An in silico Study

Molecular dynamics (MD) simulations were utilized to investigate the dynamic behavior of eukaryotic translation initiation factor 4E (eIF4E) in its apo (ligand-free) and Cap-bound (complexed with mRNA Cap) forms. Specifically, we focused on the rearrangement of critical eIF4E residues, including W102, E103, W56, and key charged residues within the alpha helix, such as lysine and arginine. Three independent 1 {micro}s MD simulations were performed for four eIF4E structures based on an available Capbound eIF4E crystal structure (PDB: 4TPW) to sample protein conformations and explore metastable states. Metastable states were successfully sampled within the 1 {micro}s trajectories for all four structures; however, 2D-root-mean-square deviation (RMSD) and free-energy landscape (FEL) analyses indicate that additional trajectory data may be needed to fully explore the conformational space. Notably, the clearest state transitions were observed in the Cap-A simulations. Our data suggests that previously reported allosteric site eIF4E inhibitor 4EGI-1 stabilized the 7mGTP-eIF4E interaction by binding to a site dorsal from the eIF4G binding site, facilitating stable protein states even after ligand removal and promoting cleaner state transitions in simulations. Root-mean-square fluctuation (RMSF) and distance analyses aligned consistently with experimental results, affirming the validity of our MD simulation system. Observations on apo and Cap eIF4E structures revealed structural changes in one of the alpha helices (i.e., H3), particularly the transition from alpha helix to loop upon Cap binding. This transition was also observed during the cap to apo transition, where residues E105-R109 underwent structural rearrangements from loop to alpha helix. These findings support the strategy of designing agents targeting critical Cap-binding residues (W56, W102, E103) and H3 lysine residues (K106, K108) to disrupt the 7mGTP-eIF4E interaction, potentially informing future drug design efforts targeting this oncogenic protein. Future work will focus on studying the apo to Cap transition using available eIF4E apo structures, such as PDB entry 2GPQ, to deepen our understanding of eIF4Es metastable states during Cap binding.

biochemistry↗

bioRxiv2021

Genomics analysis of hexanoic acid exposure in Drosophila species

Drosophila sechellia is a dietary specialist endemic to the Seychelles islands that has evolved to consume the fruit of Morinda citrifolia. When ripe, the fruit of M. citrifolia contains octanoic acid and hexanoic acid, two medium chain fatty acid volatiles that deter and are toxic to generalist insects. D. sechellia has evolved resistance to these volatiles allowing it to feed almost exclusively on this host plant. The genetic basis of octanoic acid resistance has been the focus of multiple recent studies, but the mechanisms that govern hexanoic acid resistance in D. sechellia remain unknown. To understand how D. sechellia has evolved to specialize on M. citrifolia fruit and avoid the toxic effects of hexanoic acid, we exposed adult D. sechellia, D. melanogaster and D. simulans to hexanoic acid and performed RNA sequencing comparing their transcriptional responses to identify D. sechellia specific responses. Our analysis identified many more genes responding transcriptionally to hexanoic acid in the susceptible generalist species than in the specialist D. sechellia. Interrogation of the sets of differentially expressed genes showed that generalists regulated the expression of many genes involved in metabolism and detoxification whereas the specialist primarily downregulated genes involved in the innate immunity. Using these data we have identified interesting candidate genes that may be critically important in aspects of adaptation to their food source that contains high concentrations of HA. Understanding how gene expression evolves during dietary specialization is crucial for our understanding of how ecological communities are built and how evolution shapes trophic interactions.

genomics↗