Biology subjects

Harvey, B. J.

Publications and source records attributed to Harvey, B. J..

4 recordsLinked to original sources

bioRxiv2024

Good fire: quantifying the beneficial ecosystem work of western U.S. wildfires (2010-2020)

Wildfires are integral for western US forests that have evolved with fire. Here we define "good wildfire" as areas that burn in an ecologically beneficial way, with a severity and return interval analogous to their historical fire regimes prior to European settlement. When severities match what an ecosystem historically experienced they can regulate forest structure while promoting regeneration, even in a warming climate1. We quantified the amount of forested area (i.e., deciduous, conifer, or mixed forest types) burned with a severity and frequency matching its regime, and compared that to the area of prescribed burns in forests (2010-2020). Of forests that burned in the western US, 49% of the area burned as low-moderate severity good wildfire. High severity good wildfire (in systems that historically experienced this type of fire) represented an additional 9% of forest area burned, bringing the total area of good wildfire to 58% of forested area burned. The low-moderate severity good wildfires burned 3.1 million forest ha (N = 18,061 events), more than double the 1.4 million ha of prescribed burning (N = 24,817 events on federal land) over the same period. Knowing that fires are likely going to increase in frequency and area with warming2, our key challenge will be promoting good wildfire while still protecting lives and property.

ecology↗

bioRxiv2023

Classifier for the Rapid Simultaneous Determination of Sleep-Wake States and Seizures in Mice

Sleep-wake states bi-directionally interact with epilepsy and seizures, but the mechanisms are unknown. A barrier to comprehensive characterization and the study of mechanisms has been the difficulty of annotating large chronic recording datasets. To overcome this barrier, we sought to develop an automated method of classifying sleep-wake states, seizures, and the post-ictal state in mice ranging from controls to mice with severe epilepsy with accompanying background EEG abnormalities. We utilized a large dataset of recordings, including EMG, EEG, and hippocampal local field potentials, from control and intra-amygdala kainic acid-treated mice. We found that an existing sleep-wake classifier performed poorly, even after retraining. A support vector machine, relying on typically used scoring parameters, also performed below our benchmark. We then trained and evaluated several multi-layer neural network architectures and found that a bidirectional long short-term memory-based model performed best. This Sleep-Wake and Ictal State Classifier (SWISC) showed high agreement between ground-truth and classifier scores for all sleep and seizure states in an unseen and unlearned epileptic dataset (average agreement 96.41% {+/-} SD 3.80%), and saline animals (97.77% {+/-} 1.40%). Channel elimination and feature selection provided interpretability and demonstrated that SWISC was primarily dependent on hippocampal signals, yet still maintained good performance ([~]90% agreement) with EEG alone, thereby expanding the classifiers applicability to other epilepsy datasets. SWISC enables the efficient combined scoring of sleep-wake and seizure states in mouse models of epilepsy and healthy controls, facilitating comprehensive and mechanistic studies of sleep-wake and biological rhythms in epilepsy.

neuroscience↗

bioRxiv2021

Systematic analysis of C. elegans embryo behavior reveals a stereotyped developmental progression and a rhythmic pattern of behavioral quiescence

AO_SCPLOWBSTRACTC_SCPLOWSystematic analysis of rich behavioral recordings is being used to uncover how circuits encode complex behaviors. Here we apply this approach to embryos. What are the first embryonic behaviors and how do they evolve as early neurodevelopment ensues? To address these questions, we present a systematic description of behavioral maturation for Caenorhabditis elegans embryos. Posture libraries were built using a genetically encoded motion capture suit imaged with light-sheet microscopy and annotated using custom tracking software. Analysis of cell trajectories, postures, and behavioral motifs revealed a stereotyped developmental progression. Early movement is dominated by flipping between dorsal and ventral coiling, which gradually slows into a period of reduced motility. Late-stage embryos exhibit sinusoidal waves of dorsoventral bends, prolonged bouts of directed motion, and a rhythmic pattern of pausing, which we designate slow wave twitch (SWT). Synaptic transmission is required for late-stage motion but not for early flipping nor the intervening inactive phase. A high-throughput behavioral assay and calcium imaging revealed that SWT is elicited by the rhythmic activity of a quiescence-promoting neuron (RIS). Similar periodic quiescent states are seen prenatally in diverse animals and may play an important role in promoting normal developmental outcomes.

neuroscience↗

bioRxiv2018

Pseudomonas aeruginosa PA5oct jumbo phage reduces planktonic and biofilm population and impacts its host virulence through a pseudolysogeny event

In this work we analyzed the impact of jumbo phage PA5oct on the planktonic, cell line adhered, and biofilm population of P. aeruginosa. PA5oct has a broad host-range, able to infect up to 40% of our clinical P. aeruginosa Cystic Fibrosis (CF) collection. In the airway surface liquid (ASL) model, the infection of PA5oct effectively reduced the bacterial population both adhered to epithelial cells, mucus entrapped, and dispersed. The explanation for its infectivity can also be linked to the sensitization of infected bacteria to the innate immune mechanisms and pro-inflammatory effect. Interferometry of a 72-hour old biofilm highlighted the contribution of PA5oct in biofilm matrix degradation. Interestingly, two virion-associated proteins, gp162 and gp205, have been found as putative enzymes that can degrade matrix exopolysaccharides. Two third of biofilm clones developed PA5oct phage-resistance and the cross-resistance to both LPS- and pili-dependent phages. Simultaneously, all clones resistant to phage PA5oct maintain the phage DNA within the population, strongly reducing bacterial virulence in vivo. These properties can be considered as key parameters for the application of this bacterial virus in phage therapy settings.\n\nOriginality-Significance StatementThe emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. However, this fundamental property also has implications for bacterial eradication in phage therapy settings. Here, we analyze the impact of PA5oct jumbo phage treatment of planktonic/cell line associated and sessile P. aeruginosa population in a preclinical evaluation of this phage for therapeutic applications. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population is correlated to reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This, phenomenon combined with the loss or modification of the phage receptor makes most of the phage-resistant clones significantly less pathogenic in in vivo model. During phage therapy treatment, phage-resistance is considered as an adverse effect, but our results indicate that it leads to diminished bacterial virulence and increased clearance of the infected host. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.

microbiology↗