Biology subjects

Howell, D.

Publications and source records attributed to Howell, D..

6 recordsLinked to original sources

bioRxiv2026

Conjugation-based genome engineering enables rapid prototyping and bioproduction in non-model bacteria

Non-model bacteria offer unique metabolic capabilities for sustainable bioproduction, yet their limited genetic accessibility hinders systematic strain development. Here we present conjugation-based serine recombinase-assisted genome engineering (cSAGE), a portable platform for sequential, site-specific genomic integration in transformation-resistant bacteria. Using Rhodobacter sphaeroides as a testbed, we show that genome integration fails by electroporation and is not rescued by disruption of three candidate restriction endonucleases. Conjugative delivery of the same integration vectors recovers genomic integrants at frequencies of approximately 10-4 per recipient cell, an improvement of at least five orders of magnitude over electroporation. We demonstrate site-specific genomic integration across eight bacterial hosts spanning four classes and two phyla, as well as three sequential payload integrations using a standardized, non-replicating plasmid toolkit. We then use cSAGE to install the same bioproduction pathway in two Rhodopseudomonas palustris strains: the reference strain CGA009 and the environmental isolate P4, for which genetic engineering has not previously been reported. Under anoxygenic photosynthetic growth conditions, engineered P4 produces p -vinylphenol from p -coumarate, whereas CGA009 engineered with the same construct, does not. By enabling standardized genome engineering and cross-host evaluation of bioproduction pathways, cSAGE provides a general framework for non-model strain prototyping and biotransformation discovery.

synthetic biology↗

bioRxiv2025

Adaptation of Anaplasma phagocytophilum to the tick vector is controlled by the transcriptional regulator Tr1

Rickettsial pathogens are strictly dependent on the cellular biology of their hosts for survival and replication. Predominantly transmitted by blood-feeding arthropods, these vector-borne pathogens are forced to adapt between the disparate environments of their mammalian host and arthropod vector. To achieve this, the Rickettsial bacteria Anaplasma phagocytophilum undergoes extensive transcriptional reprogramming with over 41% of its genes differentially transcribed between mammals and Ixodes scapularis ticks. How the bacterium orchestrates this dramatic transcriptional reprogramming is not understood. The gene tr1 encodes a Helix-Turn-Helix DNA-binding protein that is exclusively expressed during tick infection. Herein, we show that tr1 is essential for A. phagocytophilum survival in ticks and regulates the transcription of other genes necessary to adapt to the arthropod vector. We demonstrate that Tr1 is a DNA-binding protein and recognizes promotors of tick-specific genes in A. phagocytophilum, including secreted effector ateA, alternate components of type IV secretion system (T4SS), and membrane proteins. Our findings demonstrate that Tr1 is a master regulator of genes that are critical for A. phagocytophilum adaptation to the tick.

microbiology↗

bioRxiv2024

White adipose tissue remodeling in Little Brown Myotis (Myotis lucifugus) with white-nose syndrome

White-nose syndrome (WNS) is a fungal wildlife disease of bats that has caused precipitous declines in certain Nearctic bat species. A key driver of mortality is premature exhaustion of fat reserves, primarily white adipose tissue (WAT), that bats rely on to meet their metabolic needs during winter. However, the pathophysiological and metabolic effects of WNS have remained ill-defined. To elucidate metabolic mechanisms associated with WNS mortality, we infected a WNS susceptible species, the Little Brown Myotis (Myotis lucifugus), with Pseudogymnoascus destructans (Pd) and collected WAT biopsies for histology and targeted lipidomics. These results were compared to the WNS-resistant Big Brown Bat (Eptesicus fuscus). A similar distribution in broad lipid class was observed in both species, with [~]60% of total WAT consisting of triacylglycerides (TAGs). We found several baseline differences in WAT chemical composition between species. M. lucifugus WAT had significantly higher levels of measured TAGs ([~]30%). Higher lipid levels in E. fuscus WAT were primarily sphingomyelins and glycerophosphoethanolamines (PEs), along with glycerophospholipids (GPs) dominated by unsaturated or monounsaturated moieties and n-6 (18:2, 20:2, 20:3, 20:4) fatty acids. These differences between M. lucifugus and E. fuscus may indicate dietary differences that lead to differential "fuel" reserves that are available during torpor. Following Pd-infection, we found that perturbation to WAT reserves occurs in M. lucifugus, but not in the resistant E. fuscus. A total of 36 GPs (primarily PEs) were higher in Pd-infected M. lucifugus, indicating perturbation to the WAT structural component. In addition to changes in lipid chemistry, smaller adipocyte sizes and increased extracellular matrix deposition was observed in Pd-infected M. lucifugus. This is the first study to describe WAT lipidomic composition of bats with different susceptibilities to WNS and highlights that recovery from WNS may require repair from adipose remodeling in addition to replenishing depot fat during spring emergence.

biochemistry↗

bioRxiv2022

Antagonistic action of Siah2 and Pard3/JamC to promote germinal zone exit of differentiated cerebellar granule neurons by modulating Ntn1 signaling via Dcc

Germinal zone (GZ) exit is at the top of a cascade of events promoting the maturation of neurons and their assembly into neuronal circuits. Developing neurons and their progenitors must interpret varied niche signals like morphogens, guidance molecules, extracellular matrix, or adhesive cues to navigate GZ occupancy. How newborn neurons integrate multiple cell-extrinsic niche cues with their cell-intrinsic machinery in exiting a GZ is unknown. We establish cooperation between cell polarity-regulated adhesion and Netrin-1 signaling comprises a coincidence detection circuit repelling maturing neurons from their GZ. In this circuit, the Partitioning defective 3 (Pard3) polarity protein and Junctional adhesion molecule-C (JAM-C) adhesion protein promote, while the Seven in absentia 2 (Siah2) ubiquitin ligase inhibits, Deleted in colorectal cancer (DCC) receptor surface recruitment to gate differentiation linked repulsion to GZ Netrin-1. These results demonstrate cell polarity as a central integrator of adhesive- and guidance cues cooperating to spur GZ exit. Highlights-Netrin1 expressed in the cerebellar GZ ranges from an attractive to repulsive cue depending on differentiation status or extracellular matrix context. -Modulation of DCC expression levels impacts the nature of the Netrin1 response and GZ occupancy status. -Siah2, Pard3, and JamC function to modulate responsiveness to purified Netrin1 and cooperate with Dcc to regulate GZ exit. -Pard3 and JamC promote both basal and Netrin1 stimulated DCC surface recruitment to control GZ exit and Netrin1 repulsion

neuroscience↗

bioRxiv2020

A precautionary solution to estimation bias in shaping safe harvest boundaries

Biased estimates of population status are a pervasive conservation problem. This problem has plagued assessments of commercial exploitation of marine species and can threaten the sustainability of both populations and fisheries. We develop a computer-intensive approach to minimize adverse effects of persistent estimation bias in assessments by optimizing operational harvest measures (harvest control rules) with closed-loop simulation of resource-management feedback systems: management strategy evaluation. Using saithe (Pollachius virens), a bottom-water, apex predator in the North Sea, as a real-world case study, we illustrate the approach by first diagnosing robustness of the existing harvest control rule and then optimizing it through propagation of biases (overestimated stock abundance and underestimated fishing pressure) along with select process and observation uncertainties. Analyses showed that severe biases lead to overly optimistic catch limits and then progressively magnify the amplitude of catch fluctuation, thereby posing unacceptably high overharvest risks. Consistent performance of management strategies to conserve the resource can be achieved by developing more robust control rules. These rules explicitly account for estimation bias through a computational grid search for a set of control parameters (threshold abundance that triggers management action, Btrigger, and target exploitation rate, Ftarget) that maximize yield while keeping stock abundance above a precautionary level. When the biases become too severe, optimized control parameters- for saithe, raising Btrigger and lowering Ftarget-would safeguard against overharvest risk (<3.5% probability of stock depletion) and provide short-term stability in catch limit (<20% year-to-year variation), thereby minimizing disruption to fishing communities. The precautionary approach to fine-tuning adaptive risk management through management strategy evaluation offers a powerful tool to better shape sustainable harvest boundaries for exploited resource populations when estimation bias persists. By explicitly accounting for emergent sources of uncertainty our proposed approach ensures effective conservation and sustainable exploitation of living marine resources even under profound uncertainty. Open Research StatementData sets and code utilized for this research are available on Figshare. DOI: https://doi.org/10.6084/m9.figshare.13281266

ecology↗

bioRxiv2020

Managing Arctic predator harvest instability amplified by variable prey productivity and ocean temperature

Sustainable human exploitation of marine living resources stems from a delicate balance between short-term yield stability and long-term population persistence to achieve socioeconomic and conservation goals. However, imperfect knowledge of how oscillations in ecosystem processes regulate fluctuations in exploited populations can obscure the risk of missing management targets. We illustrate how the harvest policy to suppress short-term yield fluctuation inadvertently disrupts population cycles and yield stability of exploited, long-lived predators under stochastically fluctuating environmental forces (food availability and regional climate) using Northeast Arctic (NEA) cod (Gadus morhua, an apex predatory fish) as a case study. We use a stochastic, empirically parameterized multispecies model to simulate NEA cod population dynamics through life-history processes; Barents Sea capelin (Mallotus villosus, a pelagic forage fish) modulates cod productivity through density-dependent cannibalism-predation dynamics, whereas sea temperature regulates cod consumption, growth, and recruitment. We first test how capelin and sea temperature fluctuations regulate patterns in cod yield fluctuation and then quantitatively assess how fishing pattern designed to limit yield between-year variance (within 50-5%) perturbs cod population-catch dynamics. Simulations suggest that capelin and temperature interactively contribute to shifting cyclic patterns in cod yield fluctuation primarily through cod cannibalism-predation dynamics. Wavelet analyses further show that muffling yield variance (30 % or less) reshapes the cyclicity (shorter period and greater amplitude) of cod population size and demography, thereby becoming progressively unsynchronized with fishing pressure. Our work reveals unintended consequences of managing transient dynamics of fished populations: the interworking of population cycle destabilized by inadvertently intensifying fishing pressure, amplifying yield fluctuation and, in turn, elevating overharvest risk when not accounting for compounded effects of stochasticity in ecologically connected processes. These policy implications underscore the need for an ecosystem approach to designing ecologically sound management measures to safely harvest shared living resources while achieving socioeconomic security in increasingly more dynamic oceans in the Arctic and elsewhere.

ecology↗