Biology subjects

Brown, D. J.

Publications and source records attributed to Brown, D. J..

6 recordsLinked to original sources

bioRxiv2024

Repair of leukemia-associated single nucleotide variants via interallelic gene conversion

CRISPR-Cas9 is a useful tool for inserting precise genetic alterations through homology-directed repair (HDR), although current methods rely on provision of an exogenous repair template. Here, we tested the possibility of repairing heterozygous single nucleotide variants (SNVs) using the cells own wild-type allele rather than an exogenous template. Using high-fidelity Cas9 to perform allele-specific CRISPR across multiple human leukemia cell lines as well as in primary hematopoietic cells from patients with leukemia, we find high levels of reversion to wild-type in the absence of exogenous template. Moreover, we demonstrate that bulk treatment to revert a truncating mutation in ASXL1 using CRISPR-mediated interallelic gene conversion (IGC) is sufficient to prolong survival in a human cell line-derived xenograft model (median survival 33 days vs 27.5 days; p = 0.0040). These results indicate that IGC can be applied to numerous types of leukemia and can meaningfully alter cellular phenotypes at scale. Because our method targets single-base mutations, rather than larger variants targeted by IGC in prior studies, it greatly expands the pool of risk-increasing genetic lesions which could potentially be targeted by IGC. This technique may reduce cost and complexity for experiments modeling phenotypic consequences of SNVs. The principles of SNV-specific IGC demonstrated in this proof-of-concept study could be applied to investigate the phenotypic effects of targeted clonal reduction of leukemogenic SNV driver mutations.

cancer biology↗

bioRxiv2023

Evidence that ultrafast non-quantal transmission underlies short-latency vestibular evoked potentials.

Amniotes evolved a unique calyceal postsynaptic terminal in the vestibular organs of the inner ear that underpins quantal and non-quantal transmission at the synapse of sensory hair cells and vestibular afferent neurons. The non-quantal component is of particular interest as it includes an ultrafast synaptic current thought to underlie the exquisite synchronization of action potentials in vestibular afferent fibres to dynamic stimuli such as sound and vibration. Here we demonstrate evidence that non-quantal transmission is responsible for short latency vestibular evoked potentials (vCAPs) in the guinea pig utricle. We first show that, unlike auditory nerve responses which are completely abolished, vCAPs are insensitive to local administration of the AMPA receptor agonist CNQX. Moreover, latency comparisons between presynaptic hair cell and postsynaptic neural responses reveal that the vCAP occurs without measurable synaptic delay. Finally, using a paired-pulse stimulus designed to deplete the readily releasable pool of synaptic vesicles in hair cells, we reveal that forward masking is lacking in vestibular responses, compared to the equivalent cochlear responses. Our data support the hypothesis that the fast component of non-quantal transmission at calyceal synapses is indefatigable and responsible for ultrafast responses of vestibular organs evoked by transient stimulation. SignificanceThe mammalian vestibular system drives some of the fastest reflex pathways in the nervous system, ensuring stable gaze and postural control for locomotion on land. To achieve this, terrestrial amniotes evolved a large, unique calyx afferent terminal which completely envelopes one or more pre-synaptic vestibular hair cells, which transmits mechanosensory signals mediated by quantal and nonquantal (NQ) synaptic transmission. We present several lines of data in the guinea pig that reveal the pre-synaptic transmission of the most sensitive vestibular afferents are faster than their auditory nerve counterparts. Here, we present neurophysiological and pharmacological evidence that this vestibular speed advantage arises from ultrafast NQ electrical synaptic transmission from Type I hair cells to their calyx partners.

neuroscience↗

bioRxiv2023

Geographical Survey of the Mycobiome and Microbiome of Southern California Glassy-winged Sharpshooters

The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide-resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS1) region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide-resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide-resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices.

microbiology↗

bioRxiv2022

Vestibular Compound Action Potentials and Macular Velocity Evoked by Sound and Vibration in the Guinea Pig.

To examine mechanisms responsible for vestibular afferent sensitivity to transient air conducted sounds (ACS) and inter-aural bone conducted vibration (BCV), we performed simultaneous measurements of stimulus-evoked vestibular compound action potentials (vCAPs), utricular macula or stapes velocity, and Vestibular Microphonics (VMs) in the anaesthetized guinea pig. For short duration punctate stimuli (<1ms), the vCAP increases magnitude in close proportion to macular velocity and temporal bone (ear-bar) acceleration, rather than other kinematic variables. For longer duration stimuli, the vCAP magnitude switches from acceleration sensitive to linear jerk sensitive. vCAP input-output (IO) functions suggest primary afferent response generation has the same origins for both BCV and ACS, with similar macular velocity thresholds and IO functions for both stimuli. Frequency tuning curves evoked by tone-burst stimuli also show the vCAP increases magnitude in proportion to macular velocity, while in contrast, the VM increases magnitude in proportion to macular displacement across the entire frequency bandwidth tested. The subset of vestibular afferent neurons responsible for synchronized firing and vCAPs make calyceal synaptic contacts with type I hair cells in the striolar region of the epithelium and have irregularly spaced inter-spike intervals at rest. Present results provide new insight into mechanical and neural mechanisms underlying synchronized action potentials in these sensitive afferents, with clinical relevance for understanding the activation and tuning of neurons responsible for driving rapid compensatory reflex responses. Significant statementCalyx-bearing afferents in the utricle have the remarkable ability to fire an action potential at a precise time following the onset of a transient stimulus and provide temporal information required for compensatory vestibular reflex circuits, but specifically how transient high-frequency stimuli lead to mechanical activation of hair cells and neural responses is poorly understood. Here, we dissect the relative contributions of mechanics, hair cell transduction, and action potential generation on short-latency responses to transient stimuli. Results provide a framework for the interpretation of synchronized vestibular afferent responses, with relevance to understanding origins of myogenic reflex responses commonly used in the clinic to assay vestibular function, and vestibular short latency potentials commonly used for vestibular phenotyping in rodents.

neuroscience↗

bioRxiv2022

Investigating carbohydrate-rich feed supplements and the feeding preferences of European starlings (Sturnus vulgaris)

In the current ecological and ornithological environment in the continental United States, the European starling (Sturnus vulgaris) is one of the most common exotic bird species. After being introduced on the East Coast of the United States, the species spread rapidly across regions and ecosystems, significantly affecting the greater ecology of the nation and often disturbing local species populations. To better understand the behavior and preferences of this species, a study was devised to test the field responses of a population of European starlings in Lyon County, Kansas over a total period of 144 hours (during 48 individual observation periods) to assess and yield knowledge pertaining to their behavior and feeding patterns within a suburban environment. For this experiment, four feed alternatives (i.e., one control and three experimental) were prepared to test the impact of the utilization of carbohydrate-rich feed supplements on the degree to which the starlings would frequent a feeding location. The different feed offered to the local starlings would consist of either 300g of conventional bird feed, 200g of conventional bird feed and 100g of the supplement, 100g of conventional bird feed and 200g of the supplement, or 300g of the supplement, with the conventional bird seed acting as the control. The data suggest that the differences observed with relation to the feed alternatives were negligible, as demonstrated by the starlings preference for the different supplement concentrations (according to their feeding frequency for the four alternatives).

animal behavior and cognition↗

bioRxiv2020

A comprehensive framework for handling location error in animal tracking data

Animal tracking data are being collected more frequently, in greater detail, and on smaller taxa than ever before. These data hold the promise to increase the relevance of animal movement for understanding ecological processes, but this potential will only be fully realized if their accompanying location error is properly addressed. Historically, coarsely-sampled movement data have proved invaluable for understanding large scale processes (e.g., home range, habitat selection, etc.), but modern fine-scale data promise to unlock far more ecological information. While GPS location error can often be ignored in coarsely sampled data, fine-scale data require more care, and tools to do this have not kept pace. Current approaches to dealing with location error largely fall into two categories--either discarding the least accurate location estimates prior to analysis or simultaneously fitting movement and error parameters in a hidden-state model. In some cases these approaches can provide a level of correction, but they have known limitations, and in some cases they can be worse than doing nothing. Here, we provide a general framework to account for location error in the analysis of triangulated and trilatcralizcd animal tracking data, which includes GPS, Argos Doppler-shift, triangulated VHF, trilatcralized acoustic and cellular location data. We apply our error-modelselection framework to 190 GPS, cellular, and acoustic devices representing 27 models from 14 manufacturers. Collectively, these devices were used to track a wide range of taxa comprising birds, fish, reptiles, and mammals of different sizes and with different behaviors, in urban, suburban, and wild settings. In almost half of the tested device models, error-model selection was necessary to obtain the best performing error model, and in almost a quarter of tested device models, the reported DOP values were actually misinformative. Then, using empirical tracking data from multiple species, we provide an overview of modern, error-informed movement analyses, including continuous-time path reconstruction, home-range distribution, home-range overlap, speed, and distance estimation. Adding to these techniques, we introduce new error-informed estimators for outlier detection and autocorrelation visualization. Because error-induced biases depend on many factors--sampling schedule, movement characteristics, tracking device, habitat, etc.--differential bias can easily confound biological inference and lead researchers to draw false conclusions. We demonstrate how error-informed analyses on calibrated tracking data can provide more accurate estimates are that are insensitive to location error, and allow researchers to use all of their data.

ecology↗