Biology subjects

Walker, F. M.

Publications and source records attributed to Walker, F. M..

10 recordsLinked to original sources

bioRxiv2026

Preclinical evaluation of ixazomib for high-risk pediatric brain tumors

Background: Many of the highest risk pediatric brain cancers continue to experience poor clinical outcomes despite intensification of current multimodal therapy. Proteasome inhibition has shown preclinical promise across a range of cancer models including diffuse midline glioma (DMG), medulloblastoma, and atypical teratoid / rhabdoid tumors (ATRT), though clinically viable agents have been limited. Recent studies in adults with glioblastoma suggest that ixazomib, a second-generation proteasome inhibitor, might achieve therapeutic concentrations in the CNS, presenting the opportunity that a CNS penetrant proteasome inhibitor might be similarly leveraged for benefit in childhood brain cancers. Methods: Ixazomib was tested against cell lines and orthotopic xenograft models of DMG, Myc-amplified medulloblastoma (Myc-MB), and ATRT. RNA sequencing and LC-MS based proteomics were utilized to define functional consequences of ixazomib treatment in these models. Proteasome activity readouts were used to assess ixazomib activity across brain regions and extracranial solid organs. Results: Ixazomib demonstrates consistent cytotoxic effect across high-risk brain tumor models at low nanomolar concentrations. Ixazomib treatment activates proteostatic stress response and apoptosis. Treatment with ixazomib does not demonstrate survival benefit in orthotopic models, however, and pharmacodynamic testing suggests insufficient inhibition of proteasome activity within the CNS compared to extracranial tissues. Conclusions: While many pediatric brain tumor models demonstrate susceptibility to proteasome inhibition, ixazomib may lack sufficient blood-brain barrier penetration to be a translationally viable means of exploiting this vulnerability.

cancer biology↗

bioRxiv2026

Is a dam-altered river in the U.S. Southwest a barrier to dispersal for populations of a common lizard, Uta stansburiana?

Dams can significantly alter natural riverine systems, but their impact on movement across rivers for most terrestrial vertebrates is poorly known. The completion of Glen Canyon and Flaming Gorge dams in Arizona and Utah (southwestern United States) profoundly changed the Colorado and Green Rivers and have altered habitat for many species. The common side-blotched lizard (Uta stansburiana) offers an excellent opportunity to examine the effects of riverine impoundments on migration and gene flow in terrestrial biodiversity. To assess these effects, we collected tissue samples from 241 Uta stansburiana above and below Glen Canyon Dam and on both sides of the Colorado river at three separate study areas. We used eight microsatellite loci to estimate genetic exchange in the context of genetic diversity and structure. One study area below Flaming Gorge Dam and above Glen Canyon Dam has annual periods of warmer water temperatures and lower flows that are closer to pre-dam conditions, whereas two study areas below Glen Canyon Dam have cold water temperatures year-round, and less pronounced seasonal low flow episodes. We predicted that warmer water temperatures above Glen Canyon Dam would promote greater genetic exchange among populations than below the dam. However, we found evidence for low levels of genetic exchange between sites both above and below Glen Canyon Dam, and a moderate amount of exchange at a site below this dam where lizards could conceivably move from one side to the other. Our results imply that 1) the changes in water temperature and hydrology in dam-altered rivers are a barrier for this species even when the distance from the dam is great; and 2) genetic exchange may be dependent on river morphology. These results are relevant to other small vertebrates, particularly ectotherms, that occupy habitat proximal to a dammed river and has implications for the conservation management of impounded river systems.

zoology↗

bioRxiv2025

Targeting processive transcription for Myc-driven circuitry in medulloblastoma

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSMedulloblastoma is the most common malignant brain tumor of childhood. The highest-risk tumors are driven by recurrent Myc amplifications (Myc-MB) and experience poorer outcomes despite intensive multimodal therapy. The Myc transcription factor defines core regulatory circuitry for these tumors and acts to broadly amplify downstream pro-survival transcriptional programs. Therapeutic targeting of Myc directly has proven elusive, but inhibiting transcriptional cofactors may present an indirect means of drugging the oncogenic transcriptional circuitry sustaining Myc-MB. MethodsIndependent CRISPR-Cas9 screens were pooled to identify conserved dependencies in Myc-MB. We performed chromatin conformation capture (Hi-C) from primary patient Myc-MB samples to map enhancer-promoter interactions. We then treated in vitro and xenograft models with CDK9/7 inhibitors to evaluate effect on Myc-driven programs and tumor growth. ResultsEight CRISPR-Cas9 screens performed across three independent labs identify CDK9 as a conserved dependency in Myc-MB. Myc-MB cells are susceptible to CDK9 inhibition, which is synergistic with concurrent inhibition of CDK7. Inhibition of transcriptional CDKs disrupts enhancer-promoter activity in Myc-MB and downregulates Myc-driven transcriptional programs, exerting potent anti-tumor effect. ConclusionsOur findings identify CDK9 inhibition as a translationally promising strategy for the treatment of Myc-MB. KO_SCPLOWEYC_SCPLOW PO_SCPLOWOINTSC_SCPLOWO_LICDK9 is an intrinsic dependency in Myc-driven medulloblastoma C_LIO_LIDual CDK9/7 inhibition disrupts Myc-driven transcriptional circuitry C_LIO_LICDK9 inhibitors should be developed as pharmaceutical agents for Myc-MB C_LI IO_SCPLOWMPORTANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWOFC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWTHEC_SCPLOW SO_SCPLOWTUDYC_SCPLOWMedulloblastoma is the most common malignant brain tumor of childhood, and outcomes for high-risk subgroups remain unsatisfactory despite intensive multimodal therapy. In this study, we pool multiple independent CRISPR-Cas9 screens to identify transcriptional cofactors such as CDK9 as conserved dependencies in Myc-MB. Using Hi-C from primary patient samples, we map Myc enhancer-promoter interactions and show that they can be disrupted using inhibition of transcriptional CDKs. CDK9 inhibitor treatment depletes Myc-driven transcriptional programs, leading to potent anti-tumor effect in vitro and prolongation of xenograft survival in vivo. With a large number of CDK9 inhibitory compounds now in clinical development, this study highlights the opportunity for clinical translation of these for children diagnosed with Myc-MB.

cancer biology↗

bioRxiv2023

Lyssa excreta: Defining parameters for fecal samples as a rabies virus surveillance method

It is not possible to systematically screen the environment for rabies virus (RABV) using current approaches. We sought to determine under what conditions RABV is detectable from feces and other accessible samples from infected wildlife to broaden the number of biological samples that could be used to test for RABV. We employed a recently-developed quantitative RT-PCR assay called the "LN34 panlyssavirus real-time RT-PCR assay", which is highly sensitive and specific for all variants of RABV. We harvested and tested brain tissue, fecal, and/or mouth swab samples from 25 confirmed RABV positive bats of six species. To determine if rabies RNA lasts in feces sufficiently long post-defecation to use it as a surveillance tool, we tested fecal samples from 10 bats at the time of sample collection and after 24 hours of exposure to ambient conditions, with an additional test on six bats out to 72 hours. To assess whether we could pool fecal pellets and still detect a positive, we generated dilutions of known positives at 1:1, 1:10, 1:50, and 1:200. For six individuals for which matched brain, mouth swab, and fecal samples were tested, results were positive for 100%, 67%, and 67%, respectively. For the first time test to 24 hours, 63% of feces that were positive at time 0 were still positive after 24 hours, and 50% of samples at 72 hours were positive across all three replicates. Pooling tests revealed that fecal positives were detected at 1:10 dilution, but not at 1:50 or 1:200. Our preliminary results suggest that fecal samples hold promise for a rapid and non-invasive environmental screening system.

pathology↗

bioRxiv2023

Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy

AO_SCPLOWBSTRACTC_SCPLOWDynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. PTEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy. Using model systems of pediatric high-grade glioma, we show that rapid genome-wide reorganization of active chromatin facilitates PTEFb-mediated nascent transcriptional induction within hours of exposure to therapeutic ionizing radiation. Concurrent inhibition of PTEFb disrupts this chromatin reorganization and blunts transcriptional induction, abrogating key adaptive programs such as DNA damage repair and cell cycle regulation. This combination demonstrates a potent, synergistic therapeutic potential agnostic of glioma subtype, leading to a marked induction of tumor cell apoptosis and prolongation of xenograft survival. These studies reveal a central role for PTEFb underpinning the early adaptive response to radiotherapy, opening new avenues for combinatorial treatment in these lethal malignancies.

cancer biology↗

bioRxiv2022

Once upon a time in Mexico: Holocene phylogeography of the spotted bat (Euderma maculatum)

Holocene-era range expansions are relevant to understanding how a species might respond to the warming and drying climates of today. The harsh conditions of North American deserts have phylogenetically structured desert bat communities but differences in flight capabilities are expected to affect their ability to compete, locate, and use habitat in the face of modern climate change. A highly vagile but data-deficient bat species, the spotted bat (Euderma maculatum) is thought to have expanded its range from central Mexico to western Canada during the Holocene. With specimens spanning this latitudinal extent, we coupled phylogeography (mtDNA) with ecological niche modeling (ENM) to investigate the Holocene biogeography from the rear to leading edges. The ENM and phylogeny supported a Holocene range expansion from Mexico with increased expansion throughout the intermountain west within the last 6 kya. Long-term isolation at the southern-most margin of the range suggests one or more populations were left behind as climate space contracted and are currently of unknown status. The species appears historically suited to track shifts in climate space but differences in flight behaviors between leading edge and core-range lineages suggest that range expansions could be influenced by differences in habitat quality or climate (e.g., drought). Although its vagility could facilitate the tracking of environmental change and thereby extinction avoidance, anthropogenic pressures at the core range could still threaten the ability for beneficial alleles to expand into the leading edge.

genetics↗

bioRxiv2022

Detecting bat environmental DNA from water-filled road-ruts in upland forest

Declines in population and diversity of North American bats are rapidly occurring due to habitat loss, incidental take from various industry projects, and lethal White-nose Syndrome disease. It is critical to accurately census habitat for appropriate conservation measures, yet traditional sampling methodology, such as mist netting and acoustic recordings, can be time-intensive and biased. Instead, a passive sampling tool that does not rely on the a priori knowledge of bat roosts may provide crucial information on bat communities. In the water-limited habitats of forested uplands of the Appalachian Plateau, water-filled road-ruts are important resources for bats. Therefore, we developed an environmental DNA (eDNA) protocol to sample isolated road-ruts that may have the presence of sloughed cellular material from actively drinking bats. The detection of bat eDNA was investigated from a positive control experiment, and across 47 water samples collected in Kentucky and Ohio. Water samples were analyzed using both species-specific quantitative polymerase chain reaction (qPCR) and community metabarcoding methodologies. Using qPCR analysis, we detected eDNA from big brown bat (Eptesicus fuscus) and eastern red bat (Lasiurus borealis) from water-filled road-ruts. While the community metabarcoding approach failed to detect any bat eDNA, many non-target amphibians, birds, and mammals were identified. These results suggest eDNA found within road-ruts provides an additional detection tool for surveying biodiversity across upland forests. Additionally, the use of qPCR increased the detection of rare eDNA targets, which will be crucial for properly implementing future eDNA applications for improving bat conservation efforts across the landscape. Article impact statementEnvironmental DNA provides detection of bats from drinking sources offering a novel survey method for management and conservation efforts

ecology↗

bioRxiv2022

Advancing North: White-nosed coatis Nasua narica Range Expansion in Arizona

Over the past century, the white-nosed coati (WNC; Nasua narica) has expanded its northernmost range from the United States-Mexico border into northern Arizona. WNC are medium-sized, opportunistic omnivores that often occur in large groups ("bands") and forage on insects, fruits, and small vertebrates. We compiled data from iNaturalist, published literature, Arizona Game and Fish records, museum collections, personal communications, and our own camera trap photography to chronicle this range expansion. Historical records documented WNC populations in mountainous areas along the US-Mexican border but rarely north of Tucson, AZ. The popularity of using wildlife cameras in both research and recreation, paired with the advancement of citizen science projects like iNaturalist have generated a vast amount of new data on species distributions. With this new body of information we report the range of WNC now occurs over 400 km farther north, extending north of Flagstaff, Arizona. Recent records include occurrence in ponderosa pine forest that sustain sometimes heavy winter snow - an environment vastly different from the species normal range. The northward expansion of this meso-carnivore invites many questions about drivers of range expansion, including climate change, mesopredator release, or simple opportunism. More research into the behavior and ecology of WNC in the northern extent of their range is needed to guide understanding and potential future management of this species, its impacts, and prediction of other such range expansions.

ecology↗

bioRxiv2022

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States.

1.BackgroundDetermining the life-history traits of extinct species is often difficult from skeletal remains alone, limiting the accuracy of studies modeling past ecosystems. However, the analysis of the degraded endogenous bacterial DNA present in paleontological fecal matter (coprolites) may enable the characterization of specific traits such as the hosts digestive physiology and diet. An issue when evaluating the microbial composition of coprolites is the degree to which the microbiome is representative of the hosts original gut community versus the changes that occur in the weeks following deposition due to desiccation. Analyses of paleontological microorganisms are also relevant in the light of recent studies linking the Late Pleistocene and Early Holocene extinctions with modern-day zoonotic pathogen outbreaks. MethodsShotgun sequencing was performed on ancient DNA (aDNA) extracted from coprolites of the Columbian mammoth (Mammuthus Columbi), Shasta ground sloth (Nothrotheriops shastensis) and paleontological bison (Bison sp.) collected from caves on the Colorado Plateau, Southwestern USA. The novel metagenomic classifier MTSv, parameterized for studies of aDNA, was used to assign bacterial taxa to sequencing reads. The resulting bacterial community of coprolites was then compared to those from modern fecal specimens of the African savannah elephant (Loxodonta africana), the brown-throated sloth (Bradypus variegatus) and the modern bison (Bison bison). Both paleontological and modern bison fecal bacterial communities were also compared to those of progressively dried cattle feces to determine whether endogenous DNA from coprolites had a microbiome signal skewed towards aerobic microorganisms typical of desiccated fecal matter. ResultsThe diversity of phyla identified from coprolites was lower than modern specimens. The relative abundance of Actinobacteria was increased in coprolites compared to modern specimens, with fewer Bacteroidetes and Euryarchaeota. Firmicutes had a reduced relative abundance in the mammoth and bison coprolites, compared to the African savanna elephants and modern bison. There was a significant separation of samples in NMDS plots based on their classification as either paleontological or modern, and to a lesser extent, based on the host species. Increasingly dried cattle feces formed a continuum between the modern and paleontological bison samples. ConclusionOur results reveal that any coprolite metagenomes should always be compared to desiccated modern fecal samples from closely related hosts fed a comparable diet to determine the degree to which the coprolite metagenome is a result of desiccation versus true dissimilarities between the modern and paleontological hosts. Also, a large-scale desiccation study including a variety of modern species may shed light on life-history traits of extinct species without close extant relatives, by establishing the proximity of coprolite metagenomes with those from dried modern samples.

paleontology↗

bioRxiv2020

Relatedness and genetic structure of big brown bat (Eptesicus fuscus) maternity colonies in an urban-wildland interface provides insight into rabies transmission dynamics

Big brown bats (Eptesicus fuscus) are the bat species most frequently found to be rabid in North America and are a key source of sylvatic rabies in wildlife. Females can form summer maternity colonies in urban areas, often using access holes in the exterior of buildings to roost in relatively large numbers. In Flagstaff, Arizona, these roosts are commonly found in houses adjacent to golf courses, where habitat quality (food, water, shelter) is high for bats and for mesocarnivores such as striped skunks (Mephitis mephitis) and gray foxes (Urocyon cinereoargenteus). Periodic rabies outbreaks in Flagstaff involving all three of these mammals are primarily caused by an E. fuscus variant of the disease. However, little is known about E. fuscus social behavior during the summer months and how it may drive space use and hence disease exposure to conspecifics and mesocarnivores. To address this knowledge gap, we collected 88 unique genetic samples via buccal swabs from E. fuscus captured at four maternity roosts surrounding a golf course during summer of 2013. We used 7 microsatellite loci to estimate genetic relatedness among individuals and genetic structure within and among colonies in order to infer whether females selected roosts based on kinship, and used genetics and radio telemetry to determine the frequency of roost switching. We found roost switching through genetics (two mother and adult daughter pairs at the same and different roosts) and telemetry, and no evidence of elevated genetic relatedness within colonies or genetic structure between colonies. These results have important implications for disease transmission dynamics in that social cohesion based on relatedness does not act to constrain the virus to a particular roost area. Instead, geographic mobility may increase disease exposure to neighboring areas. We discuss mitigating actions for bat conservation and public health.

ecology↗