Biology subjects

Davis, D. A.

Publications and source records attributed to Davis, D. A..

11 recordsLinked to original sources

bioRxiv2025

Differential Capture Modalities of Insect Traps Produce Contrasting Biodiversity Patterns

Describing insect community and population trends is essential to their conservation. To assess insect populations and communities and identify potential drivers of change in insect populations, we often need to measure in a variety of ways and in a variety of ecosystems. Insect sampling is not standardized: data is frequently collected via different types of insect traps with different targets and modes of capture to sample the insect community. However, different traps may identify contrasting ecological signals, depending on their structure, deployment, and their effective range, and further, these differences may interact with the habitats they are deployed in. Here, we aim to assess the consistency of biodiversity patterns produced from different trapping methods deployed in array across several habitats. We investigated three trapping methods: an ant bait trap, a malaise trap, and a fermentation trap. We deployed these traps in a suburban forested area and at a restored forest. We computed richness and relative abundance of insects captured in each trap and assessed community compositional differences between traps and habitats. We found that each trap type produced differential patterns of richness, abundance, and composition from each other, and these patterns also varied between sites for most trap types. The contrasting patterns observed among traps is likely due to differing effective capture ranges of each trap; traps with smaller effective capture ranges were more sensitive to local habitat conditions than traps with broader effective capture ranges.

ecology↗

bioRxiv2024

The Elevated Expression of ORF75, a Lytic KSHV Gene, in Kaposi Sarcoma Lesions is Driven by a GC-rich DNA cis Element in its Promoter Region

The spindle cells of Kaposi sarcoma (KS) lesions primarily express Kaposi sarcoma herpesvirus (KSHV) latent genes with minimal expression of lytic genes. However, recent transcriptome analyses of KS lesions have shown high expression of KSHV open reading frame (ORF) 75, which is considered a late lytic gene based on analyses in primary effusion lymphoma (PEL) lines. ORF75 encodes a pseudo-amidotransferase that is part of the viral tegument, acts as a suppressor of innate immunity, and is essential for viral lytic replication. We assessed a representative KS lesion by RNAscope and found that ORF75 RNA was expressed in the majority of latency-associated nuclear antigen (LANA)-expressing cells. Luciferase fusion reporter constructs of the ORF75 promoter were analyzed for factors potentially driving its expression in KS. The ORF75 promoter construct showed high basal transcriptional activity in vitro in endothelial cells, mediated by a proximal consensus specificity protein 1 (Sp1) (GGGGCGGGGC) element along with two distal CCAAT boxes. Sp proteins formed complexes with the proximal consensus Sp1 element to activate ORF75 promoter transcription. We also found evidence that a repressive factor or factors in B cells, but not endothelial or epithelial cells, interacted with more distal elements in the ORF75 promoter region to repress constitutive ORF75 expression in B cells. Alternate forms of Sp1 were found to accumulate during latency and showed substantial enrichment during viral lytic replication in PEL cells and infected endothelial cells, but their functional significance is unclear. We also found that ORF75 can in turn upregulate its own expression and that of other KSHV genes. Thus, while ORF75 acts primarily as a lytic gene in PEL cell lines, Sp proteins induce substantial constitutive ORF75 transcription in infected endothelial cells and this can account for its high expression in KS lesions. Author SummaryIn our study, we explored KSHV ORF75, a tegument protein that is increasingly being appreciated as playing a vital role in KSHV replication and inactivating the innate immune response. ORF75 is characterized as a late lytic protein but has been recently found to be consistently expressed in Kaposis sarcoma (KS) lesions, which generally express only latent KSHV genes. Our findings reveal that ORF75 is constitutively expressed in endothelial and epithelial cells, and to a lesser extent B-cells. We found that constitutive expression of ORF75 is largely mediated by specificity (Sp) proteins binding to a proximal Sp1 site in the ORF75 promoter region. Moreover, we found that the lower expression of ORF75 in KSHV-infected B cells is due to suppressive factors acting at a more distal region of the ORF75 promoter. We further found that ORF75 can enhance expression of its own RNA as well as that of several other KSHV proteins, including replication and transcription activator (RTA) and latency associated nuclear antigen (LANA). This constitutive expression of ORF75, a late lytic gene, can explain how it can play such an important role in the earlier steps in KSHV lytic activation and underscores the importance of this gene.

microbiology↗

bioRxiv2023

Tor1 dysfunction promotes phenotypic diversity in the asexual fungus Candida albicans

Genetic variation is a primary contributor to phenotypic variation within a population. In asexual eukaryotes however, it is unclear how, or if, genetic variation is generated and maintained to promote phenotypic variation. C. albicans, an asexual fungus that causes opportunistic infections in susceptible hosts, has several phenotypic switching systems, including the colony morphology phenotypic switching (CMPS) system. CMPS, a penetrant change in colony morphology on solid medium in vitro, is associated with incipient or fulminant clinical disease. CMPS results in the alteration of additional virulence properties, including drug resistance, that are not tightly correlated with colony morphology. Importantly, it is unknown whether CMPS is a regulated or stochastic process. We found that specific mutants affecting the Target of Rapamycin (TOR) pathway showed an increase in CMPS frequency and CMPS in these mutant backgrounds was associated with changes in rapamycin sensitivity. We also identified growth conditions that promoted CMPS in clinical strains and found that CMPS in these backgrounds was also linked to the TOR pathway through changes in rapamycin sensitivity. These results demonstrate that CMPS promotes phenotypic variation through the TOR pathway, supporting a model that this is a regulated process. Since the TOR growth control pathway is conserved throughout the eukarya, the identification of TOR as a phenotypic diversity regulator likely has broad implications.

genetics↗

bioRxiv2023

Cell Type Specific CAG Repeat Expansion and Toxicity of Mutant Huntingtin in Human Striatal and Cerebellar Cell Types

Brain region-specific degeneration and somatic expansions of the mutant Huntingtin (mHTT) CAG tract are key features of Huntingtons disease (HD). However, the relationships between CAG expansions, death of specific cell types, and molecular events associated with these processes are not established. Here we employed fluorescence-activated nuclear sorting (FANS) and deep molecular profiling to gain insight into the properties of cell types of the human striatum and cerebellum in HD and control donors. CAG expansions arise in striatal medium spiny neurons (MSNs) and cholinergic interneurons, in cerebellar Purkinje neurons, and at mATXN3 in MSNs from SCA3 donors. CAG expansions in MSNs are associated with higher levels of MSH2 and MSH3 (forming MutS{beta}), which can inhibit nucleolytic excision of CAG slip-outs by FAN1 in a concentration-dependent manner. Our data indicate that ongoing CAG expansions are not sufficient for cell death, and identify transcriptional changes associated with somatic CAG expansions and striatal toxicity.

neuroscience↗

bioRxiv2023

Layer 5a Corticostriatal Projection Neurons are Selectively Vulnerable in Huntington's Disease

The properties of the cell types that are selectively vulnerable in Huntingtons disease (HD) cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance in CNS circuitry have not been delineated. Here we employed serial fluorescence activated nuclear sorting (sFANS), deep molecular profiling, and single nucleus RNA sequencing (snRNAseq) to demonstrate that layer 5a pyramidal neurons are vulnerable in primary motor cortex and other cortical areas of HD donors. Extensive mHTT-CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layer 6a, layer 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify the vulnerable layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somatic mHTT-CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in the HD cerebral cortex.

neuroscience↗

bioRxiv2022

Transcriptome and chromatin accessibility landscapes across 25 distinct human brain regions expand the susceptibility gene set for neuropsychiatric disorders

Brain region- and cell-specific transcriptomic and epigenomic molecular features are associated with heritability for neuropsychiatric traits, but a systematic view, considering cortical and subcortical regions, is lacking. Here, we provide an atlas of chromatin accessibility and gene expression in neuronal and non-neuronal nuclei across 25 distinct human cortical and subcortical brain regions from 6 neurotypical controls. We identified extensive gene expression and chromatin accessibility differences across brain regions, including variation in alternative promoter-isoform usage and enhancer-promoter interactions. Genes with distinct promoter-isoform usage across brain regions are strongly enriched for neuropsychiatric disease risk variants. Using an integrative approach, we characterized the function of the brain region-specific chromatin co-accessibility and gene-coexpression modules that are robustly associated with genetic risk for neuropsychiatric disorders. In addition, we identified a novel set of genes that is enriched for disease risk variants but is independent of cell-type specific gene expression and known susceptibility pathways. Our results provide a valuable resource for studying molecular regulation across multiple regions of the human brain and suggest a unique contribution of epigenetic modifications from subcortical areas to neuropsychiatric disorders.

neuroscience↗

bioRxiv2022

Single-cell Transcriptomic Atlas of the Human Substantia Nigra in Parkinson's Disease

Parkinsons disease (PD) is a common and complex neurodegenerative disorder. Loss of neuromelanin-containing dopaminergic (DA) neurons in the substantia nigra (SN) is a hallmark of PD neuropathology; the etiology of PD remains unclear. Single-cell (-nucleus) RNA sequencing (sc or snRNAseq) has significantly advanced our understanding of neurodegenerative diseases including Alzheimers, but limited progress has been made in PD. Here we generated by far the largest snRNAseq data of high-quality 315,867 nuclei from the human SN including 9 healthy controls and 23 idiopathic PD cases across different Braak stages. Clustering analysis identified major brain cell types including DA neurons, excitatory neurons, inhibitory neurons, glial cells, endothelial, pericytes, fibroblast and T-cells in the human SN. By combining immunostaining and validating against the datasets from independent cohorts, we identified three molecularly distinct subtypes of DA-related neurons, including a RIT2-enriched population, in human aged SN. All DA neuron subtypes degenerated in PD, whereas the composition of non-neuronal cell clusters including major glial types showed little change. Our study delineated cell-type-specific PD-linked gene expression in the SN and their alterations in PD. Examination of cell-type-based transcriptomic changes suggests the complexity and diversity of molecular mechanisms of PD. Analysis of the remaining DA neurons of the three subtypes from PD demonstrated alterations of common gene sets associated with neuroprotection. Our findings highlight the heterogeneity of DA neurons in the human SN and suggest molecular basis for vulnerability and resilience of human DA neurons in PD. Our cohort thus provides a valuable resource for dissecting detailed mechanisms of DA neuron degeneration and identifying new neuroprotective strategies for PD.

neuroscience↗

bioRxiv2021

Selective Laser Sintering of a Photosensitive Drug: Impact of Processing and Formulation Parameters on Degradation, Solid-State, and Quality of 3D Printed Dosage Forms

This research study utilized a light-sensitive drug, nifedipine (NFD), to understand the impact of processing parameters, and formulation composition on drug degradation, crystallinity, and quality attributes (dimensions, hardness, disintegration time) of selective laser sintering (SLS) based 3D printed dosage forms. Selective laser sintering (SLS), in most cases, uses an ultraviolet laser source, and drugs tend to absorb radiation at varying intensities around this wavelength (455 nm). This phenomenon may lead to chemical degradation, and solid-state transformation, which was assessed for nifedipine in formulations with varying amounts of vinyl pyrrolidone-vinyl acetate copolymer (Kollidon(R) VA 64) and potassium aluminum silicate-based pearlescent pigment (Candurin(R)), processed under different SLS conditions in the presented work. After preliminary screening Candurin(R), surface temperature (ST), and laser speed (LS) were identified as the significant independent variables. Further, using the identified independent variables a 17-run, randomized, Box-Behnken design was developed to understand the correlation trends and quantify the impact on degradation (%), crystallinity, quality attributes (dimensions, hardness, disintegration time) employing qualitative and quantitative analytical tools. The design of experiments (DoE) and statistical analysis observed that LS and Candurin(R) (%wt) had a strong negative correlation on drug degradation, hardness, and weight, whereas ST had a strong positive correlation with, drug degradation, amorphous conversion, and hardness of the 3D printed dosage form. From this study, it can be concluded that formulation and processing parameters have a critical impact on stability and performance; hence these parameters should be evaluated and optimized before exposing light-sensitive drugs to the SLS processes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/439089v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1e3dd02org.highwire.dtl.DTLVardef@c2bfaforg.highwire.dtl.DTLVardef@1b6b712org.highwire.dtl.DTLVardef@ad35fd_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2021

Regulation of the Dimerization and Activity of SARS-CoV-2 Main Protease through Reversible Glutathionylation of Cysteine 300

SARS-CoV-2 encodes main protease (Mpro), an attractive target for therapeutic interventions. We show Mpro is susceptible to glutathionylation leading to inhibition of dimerization and activity. Activity of glutathionylated Mpro could be restored with reducing agents or glutaredoxin. Analytical studies demonstrated that glutathionylated Mpro primarily exists as a monomer and that a single modification with glutathione is sufficient to block dimerization and loss of activity. Proteolytic digestions of Mpro revealed Cys300 as a primary target of glutathionylation, and experiments using a C300S Mpro mutant revealed that Cys300 is required for inhibition of activity upon Mpro glutathionylation. These findings indicate that Mpro dimerization and activity can be regulated through reversible glutathionylation of Cys300 and provides a novel target for the development of agents to block Mpro dimerization and activity. This feature of Mpro may have relevance to human disease and the pathophysiology of SARS-CoV-2 in bats, which develop oxidative stress during flight.

microbiology↗

bioRxiv2019

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

Single-cell technologies enable measure of unique cellular signatures, but are typically limited to a single modality. Computational approaches allow integration of diverse single-cell datasets, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells in tissues, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied it to post-mortem human frontal cortex tissue. We developed a computational framework to validate fine-grained cell types using multi-modal information and assessed the effectiveness of computational integration methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling prediction of cell types with causal roles in disease.

genomics↗

bioRxiv2018

Robust single-cell DNA methylome profiling with snmC-seq2

Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artifactual reads, enhanced throughput, as well as increased library complexity and coverage uniformity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large scale single-cell epigenomic studies.

genomics↗