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Molecular mechanisms regulating swarming motility in Bacilli
No full textParashar, Vijay K.Bacterial motility increases the odds of survival by allowing bacteria to colonize new niches, evade predators, and resist antibiotics. Specifically, motile cells are most resistant to antimicrobials when they undergo a type of surface movement called swarming motility. To swarm bacteria must increase their number of flagella which in Bacillus subtilis is controlled by the flagella chemotaxis (fla/che) operon. This operon is regulated by the master regulator of swarming motility, SwrA, and the response regulator DegU that binds to the fla/che promoter inducing expression of flagellar basal bodies. However, swarming motility can be inhibited through the adaptor-mediated degradation of SwrA by the protease LonA and its adaptor SmiA. Together, the transcriptional and translational regulation modulate the production of flagella needed for swarming, but how these processes function at the molecular level remain unclear. Here we identify that DegU tetramerizes on DNA in the presence of SwrA potentially positioning it to interact with the ⍺CTD of RNA polymerase. Furthermore, we structurally characterize SwrA and identify key conserved residues important for its transcriptional and swarming activity. Finally, we evaluate the interactions and oligomeric states of the post-translational complex identifying that SmiA interacts with both SwrA and LonA N-terminal domain (LonANTD) and that it forms heterodimers with LonANTD. Overall, our work expands and updates the transcriptional and translational molecular mechanisms of swarming regulation in Bacilli.University of Delaware, Department of Medical and Molecular SciencesPh.D
The Role of Land and Natural Resources in Negotiating Peace Agreements
No full textThis article was originally published in Negotiation Journal. The version of record is available at: https://doi.org/10.1162/ngtn_a_00017.
© 2025 Presidents and Fellows of Harvard College. Published under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. For a full description of the license, please visit https://creativecommons.org/licenses/by/4.0/legalcode.Drawing on the growing genre of literature on “environmental peacebuilding,” this article develops a qualitative model of how land and natural resources (including minerals, water, forests, and agricultural products) contribute to the framing of conflicts and how they might contribute to their resolution. We considered twelve cases of peace processes in which land and resources played a role and developed a causal link typology of the nexus between natural resources and conflict. Based on extensive archival research and interviews, we then developed a series of causal variables and pathways that were synthesized into our qualitative model—the Peace and Natural Resource Nexus (PNRN) Model. Our analysis suggests that there are opportunities for making peace through a nexus with natural resources and for making peace agreements more robust with greater attention to natural resource linkages even if they might not be the dominant cause of conflict. Attention to the role of natural resources in conflicts and the inclusion of environmental and natural resource factors in the negotiation of peace agreements are thus likely to be advantageous across a wide spectrum of conflicts
Transcriptome Meta-Analysis Uncovers Cell-Specific Regulatory Relationships in Embryonic, Juvenile, Adult, and Aged Mouse Lens Epithelium and Fibers
No full textThis article was originally published in Investigative Ophthalmology & Visual Science. The version of record is available at: https://doi.org/10.1167/iovs.66.4.42.
Copyright 2025 The Authors.
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/).Purpose: The lens transcriptome has been examined using microarrays and RNA-sequencing (RNA-seq). These omics data are the basis of the bioinformatics web-resource iSyTE that has identified new genes involved in lens development and cataract. The lens predominantly contains epithelial and fiber cells, and yet, presently, iSyTE is based on whole lens data. To gain cell-specific regulatory insights, we meta-analyzed isolated epithelium and fiber transcriptomes from embryonic/postnatal, adult and aged lenses.
Methods: Mouse lens epithelium and fiber transcriptome public datasets at embryonic (E) and postnatal (P) stages E12.5, E14.5, E16.5, E18.5, P0.5, P0, P5, P13, and age one month, three months, six months, and two years were analyzed. Microarray or RNA-seq data were analyzed by appropriate methods and compared to other resources (e.g., Cat-Map, CompBio).
Results: Across all RNA-seq datasets examined, 2466 genes are differentially expressed between epithelium and fibers, of which 106 are cataract-linked. Gene ontology enrichment validates epithelial and fiber expression, corroborating the meta-analysis. Whole embryonic-body–in silico subtraction and other analyses identify several new high-priority epithelial- and/or fiber-enriched genes (e.g., Casz1, Ell2). Furthermore, new insights into cell-specific regulatory processes at distinct stages are identified (e.g., ribonucleoprotein regulation in E12.5 epithelium). Finally, this data is made accessible at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/).
Conclusions: This spatiotemporal transcriptome meta-analysis comprehensively informs on epithelium- and fiber-specific regulatory processes in developing, adult and aged lenses. Notably, it includes the first description of an embryonic stage (i.e., E12.5) representing early primary fiber differentiation, thus informing on the initial transcriptome changes as lens cell-types are readily distinguishable.Supported by National Institutes of Health [R01 EY021505 and R01 EY036923] to S.L. Bioinformatics support from the University of Delaware was made possible through funding from the State of Delaware and National Institutes of Health / National Institute of General Medical Sciences INBRE Program Grant [P20 GM103446]. M.D. and L.P. were supported by a grant from Association Retina France, CNRS PICS.
Disclosure: M. Duot, None; S.Y. Coomson, None; S.K. Shrestha, None; M.V.M.K. Nagulla, None; Y. Audic, None; R.A. Barve, None; H. Huang, None; C. Gautier-Courteille, None; L. Paillard, None; S.A. Lachke, Non
The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles
No full textThis article was originally published in Gut Microbes. The version of record is available at: https://doi.org/10.1080/19490976.2025.2568706
© 2025 The Author(s). Published with license by Taylor & Francis Group, LLC. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.Understanding gut–host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and mini-mal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host–microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust tran-scriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host–microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.This work was partially supported by the USDA National Institute of Food and Agriculture Animal Health Grant No.102214
Does improving early parenting practices optimize white matter and global structural network maturation? A randomized controlled trial
No full textDozier, MaryA high-quality early parenting environment, involving a sensitive and nurturing caregiver, has a profound, lasting impact on human development. In contrast, exposure to childhood maltreatment jeopardizes brain development and heightens risks for developing psychopathology later in life. If improving the early parenting environment alters the neural developmental trajectory following experiences of childhood maltreatment, then we may be able to mitigate the risks for mental health problems. By leveraging the longitudinal follow-up data of a randomized controlled trial of the Attachment and Biobehavioral Catch-up (ABC) intervention, the present study sought to understand if ABC participation during infancy altered the developmental trajectories of white matter microstructure and global network characteristics, relative to a control intervention. A low-risk sample without prior history of maltreatment was included for reference. The growth trajectories of commissural, projection, and association fibers, as well as graph density, global efficiency, and small worldness were examined. Results indicated that ABC adolescents exhibited a nonlinear trajectory of white matter development, marked by an initial decline followed by later increases in fractional anisotropy (FA), suggesting extended neuroplasticity. Conversely, control and low-risk adolescents exhibited more accelerated maturation, with linear increases in FA and earlier signs of myelination compared to ABC. At the global level, ABC adolescents maintained stable levels of global efficiency and small worldness over time, while control and low-risk youth showed age-related declines. The findings highlight the potential for early sensitive and nurturing parenting to foster neuroplasticity and support adaptive reorganization.University of Delaware, Department of Psychological and Brain SciencesPh.D
Coherent uplink and downlink communications in RF-photonic distributed MIMO systems for 6G mmWave
No full textQi, Xiao-FengPrather, Dennis W.This thesis presents multi-user beamspace processing techniques for both uplink and downlink in a distributed multiple-input multiple-output (MIMO) RF-photonic system operating at millimeter wave (mmWave) frequencies. For the uplink, a novel Beamspace Interference Rejection Combining (BIRC) algorithm is proposed to address the limitations of conventional interference rejection combining (IRC) techniques in dense electromagnetic (EM) environments. Traditional element-space IRC suffers performance degradation as the array size increases and the element-wise signal-to-noise ratio (SNR) during channel state information (CSI) estimation decreases. The BIRC algorithm overcomes these challenges by performing both CSI estimation and interference suppression in a reduced-dimensional beamspace, derived through the spatial Fourier transform and power-based beam selection, and implemented in the analog-photonic domain. This approach improves the robustness of CSI and reduces the dependence on high-speed RF chains. Simulations using the NYUSIM channel model demonstrate that BIRC outperforms its element-space counterpart, with performance gains growing with array size. ☐ For the downlink, the thesis introduces an RF-photonic MIMO architecture that enables coherent beamforming across widely distributed antennas, supporting wideband, multi-user, and multi-beam transmission. A centralized optical local oscillator (LO) is distributed to maintain phase and frequency coherence across antennas separated by tens of kilometers. Mathematical formulations establish the foundations of IQ modulation and the implementation of beamforming weights in the optical domain using phase and amplitude control. The experimental implementation and validation of various precoding schemes show strong alignment with simulation results, confirming the feasibility of coherent downlink transmission using distributed antennas connected via long-distance fronthaul. In addition, the beam squint effect is analyzed in simulation, demonstrating noticeable performance degradation when a single-frequency precoder is applied to wideband signals. ☐ A circularly symmetric cell-free (CF) MIMO system model is introduced to formulate and evaluate the system-level performance of a cell-free architecture, where multiple access points (APs) are distributed along a circular perimeter to serve users located within a concentric region of interest. A sum capacity metric is used for performance validation and is shown to closely follow the beamforming-based sum rate. Further simulation analysis demonstrates the cumulative distribution function (CDF) of the sum capacity while varying the inter-AP angle. The results demonstrate that performance improves with increased inter-AP angle due to enhanced spatial diversity. To validate this relationship, the best- and worst-performing user equipment (UE) combinations from Monte Carlo simulations are identified and visualized. Additionally, a beam selection algorithm based on volume maximization is introduced for the RF-photonic cell-free MIMO system. The proposed algorithm is compared against several existing algorithms, including the Interference-Aware Beam Selection (IA-BS) algorithm, brute-force search, maximum-power-based selection, and full-beamspace (i.e., fully digital) methods.University of Delaware, Department of Electrical and Computer EngineeringM.S.E.C.E
Metabolism, size, and environmental influences on vision in the fiddler crab, Minuca pugnax
No full textCohen, Jonathan H.For many organisms, vision is a fundamental sensory modality influencing behaviors such as photoperiod perception, predator avoidance, and social interactions. In fiddler crabs, visual function is closely linked to ecological need, which influences key optical and energetic properties that may affect visual performance. This study explores how metabolism, morphology, and environmental parameters shape key aspects of vision in the fiddler crab, Minuca pugnax. ☐ I assessed metabolic rate, temporal resolution of vision, irradiance sensitivity, and eye morphometrics across a range of masses in M. pugnax. To measure metabolic rate, I used the proxies of dry mass-adjusted oxygen consumption rate and tissue mass-adjusted oxygen consumption rate, both of which decreased with an increase in the respective mass unit used. For temporal resolution of vision, I developed a new method of analysis using electroretinographic data to measure critical flicker fusion frequency (CFF) using a Lomb-Scargle periodogram that I then applied to M. pugnax. Electroretinography was also utilized for irradiance sensitivity to determine logK as a parameter to measure sensitivity. Both irradiance sensitivity and temporal resolution increased with metabolic rate and decreased with mass, irradiance sensitivity being an unexpected trend. Finally, histological analysis of M. pugnax eyes determined that all aspects of a compound eye facet increase with mass, which was an expected trend. Optical sensitivity values obtained from morphological measurements of the eyes were also found to increase with mass. Collectively, these findings suggest that smaller crabs have an increased need for visual speed due to faster movement relative to their body size and being more vulnerable to predators. These smaller crabs have a heightened metabolic capacity per unit body mass and smaller eyes to support this visual performance. ☐ To understand the influence of chronic temperature acclimation on metabolism and vision in M. pugnax, I applied the relationship between metabolic rate and temporal resolution of vision to a latitudinal study, as latitudinal plasticity in metabolic rate is already known to exist in fiddler crabs. Air temperature for National Estuarine Research Reserve sites in Narragansett Bay, Rhode Island; St. Jones, Delaware; and North Inlet-Winyah Bay, South Carolina, showed increased mean but decreased variability with decreasing latitude. I collected M. pugnax from near these three locations and conducted respirometry and critical flicker fusion frequency experiments at 15ºC, 20ºC, and 25ºC. As latitude increased, M. pugnax populations upregulated metabolic capacity and were less thermally sensitive, consistent with their colder and more variable chronic thermal acclimation conditions. CFF values showed no statistical significance across location or temperature aside from an increase in CFF with temperature in the southernmost population, suggesting that vision is less plastic than metabolism. Other factors, such as morphological or energetic adaptations to deal with ecological pressures, may keep this constant across latitudes. ☐ This study describes both the energetic and morphological influences on vision in M. pugnax and how these factors are shaped by acclimatization. As climate change continues to raise the temperatures of coastal marshes, the physiology of organisms that live in them will likely also be affected similarly. This study’s focus on metabolic plasticity and visual performance under varying thermal conditions provides insights into how these crabs may adapt to a changing climate. By understanding these physiological responses, we can better predict the resilience of M. pugnax and similar species to future environmental changes, informing conservation strategies for coastal ecosystems.University of Delaware, School of Marine Science and PolicyM.S
The children's interpersonal mattering at school scale: a psychometric exploration
No full textCarey, Roderick L.This dissertation contributes to the conceptual framework of mattering, a social-psychological construct reflecting one’s sense significance to others, by empirically demonstrating whether it can be quantitatively assessed in elementary school children. Despite mattering’s essential role in shaping social, emotional, and mental wellbeing, no validated scales exist for children. This dissertation addresses this gap by centering public school elementary students (in Grades 3-5) and ensuring the applicability of the Children’s Interpersonal Mattering at School Scale. For this dissertation, I developed the Children’s Interpersonal Mattering at School Scale, which contains subscales assessing Mattering to Teachers and Mattering to Friends. I piloted the scale with 447 elementary school students across four public schools (38% third graders, 32% fourth graders, 30% fifth graders). Analyses combined Rasch modeling (to evaluate structural validity) and structural equation modeling (SEM; to test convergent validity). The Rasch modeling results demonstrated strong psychometric properties, which confirms that the scale’s internal structure aligns with mattering’s conceptual framework. The SEM results further supported the measure’s validity, with subscales correlating significantly with self-esteem. This dissertation makes significant contributions to the field. First, it establishes mattering as a measurable and developmentally relevant construct for elementary students, extending its conceptual framework beyond adolescent and adult populations. It also provides education stakeholders, such as researchers, with a scale to assess students’ sense of mattering to specific people in their school environment.University of Delaware, Department of Human Development and Family SciencesPh.D
Kent County Groundwater Monitoring Project: Hydrogeology and Salinization Dynamics of Eastern Kent County
No full textSalinization can be a critical water quality problem in coastal aquifers. This is especially acute in coastal Delaware, where groundwater is the main source of fresh water and increasing population and irrigation are placing growing demands on water resources. Most farming operations and many private residences east of Dover toward the Delaware Bay rely on the shallow unconfined Columbia aquifer for fresh water. Additionally, the City of Dover operates a Columbia aquifer water supply wellfield in this area.
To investigate locations in eastern Kent County, Delaware that were previously identified as being at high risk for saltwater intrusion, we collected groundwater level and salinity data from newly installed and existing monitoring wells and test wells, tidal surface water gages, and irrigation ponds throughout the area. Our work identified several processes that contribute to salinization in the east Dover area, including irrigation pumping near tidal creeks and marshes and ground surface inundation during high tides and storms. Most observations were a combination of more than one process occurring simultaneously. This information has been communicated to stakeholders, some of whom have modified their water supply system or pumping schedule to reduce the risk of salinization. The results of this study will help predict future conditions in light of expected sea-level rise.
We found that the hydrogeologic framework plays an important role in determining the location and movement of the saltwater-freshwater interface in eastern Kent County. Discontinuous muddy beds are more prevalent at shallow depths in the Columbia aquifer and divide the aquifer into both shallow unconfined and deeper semiconfined portions. At the marsh-upland boundary and near tidal streams, groundwater in the shallow portion of the Columbia aquifer is a mixing zone of fresh groundwater and saline surface water. Salinity in groundwater here depends on a number of dynamic forces that affect the hydraulic gradient and subsequently the amount of bayward freshwater flux. During this study, we found that pumping for irrigation from wells and ponds shifts the freshwater-saltwater interface in the shallow portion of the aquifer inland and can allow saltwater to migrate into the well or pond.
Water levels indicate flow patterns are affected by irrigation, tides, and precipitation. In areas where there were no or few shallow confining layers, we observed salty water migrating into the shallow Columbia aquifer during storm events where surface water flooded the ground surface and infiltrated to the water table. However, shallow muddy layers appear to prevent salty water from migrating downward into the deeper semiconfined aquifer during inundation events such as spring high tides and storm surge. We did not encounter the freshwater-saltwater interface in wells screening deeper portions of the Columbia aquifer
