Biology subjects

Parker, D. M.

Publications and source records attributed to Parker, D. M..

12 recordsLinked to original sources

bioRxiv2025

Characterization of hippocampal subfields using histology-based annotated postmortem MRI: Lessons for in vivo segmentation II

High-resolution in vivo magnetic resonance imaging (MRI) of hippocampal subfields is a rapidly advancing field due to their implication in cognition, disorder, and disease. Hippocampal subfield segmentation on in vivo MRI is generally guided by postmortem reference material, which has been limited by small sample sizes that preclude comprehensive characterization of subfield border locations and their variability. Addressing this, we characterized hippocampal subfield border variability in two ultra-high-resolution postmortem MRI datasets with combined annotated histological sections, including cases with and without dementia. We examined: 1) the order of appearance and disappearance of subfields along the long axis of the hippocampus; 2) the order of appearance and disappearance of subicular subregions; 3) the medial-lateral position of subicular subregional boundaries along the hippocampal body; 4) the location of the CA3 relative to hippocampal head digitations; 5) the subfield borders in the hippocampal body relative to a volume proportion of the dark band; and 6) the association of hippocampal length and subiculum-CA1 border location with diagnosis, demographic factors, and factors related to postmortem imaging. Our findings reaffirmed that there is a consistent order of appearance and disappearance of subfields in the hippocampal head and tail, respectively. The subicular subregions exhibited a first in, last out order of appearance and disappearance, and pre/parasubiculum consistently occupied half of the subicular complex in coronal slices throughout the hippocampal body. Hippocampal head digitations were not a reliable landmark for CA3 appearance, but SRLM proportionality did offer a potentially consistent approach for estimating CA2 and CA3 subfield borders in relation to the hippocampal border. No clear relationship was found between the anatomical features and diagnosis, demographic factors, and factors related to postmortem imaging. These findings have implications for the development and harmonization of hippocampal subfield segmentation protocols and interpretation of high-resolution functional MRI studies of the human hippocampus.

neuroscience↗

bioRxiv2025

The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in early Caenorhabditis elegans embryos

The elimination of maternal mRNAs is an essential feature of the maternal-to-zygotic transition. We report an essential pathway that clears many maternal transcripts from early C. elegans embryos using the Rbfox-related SPN-4 RNA-binding protein as a specificity factor and the CCR4-NOT deadenylase complex as an effector. We biochemically identified SPN-4-associated mRNAs from late-stage oocytes and found that the set of SPN-4-associated transcripts is enriched for maternal mRNAs that undergo early decay. Single-molecule fluorescence in situ hybridization experiments established that many SPN-4-associated mRNAs fail to be eliminated in the absence of SPN-4. In the 3UTRs of two target mRNAs, we identified Rbfox motifs that are required for SPN-4-dependent clearance in vivo and bind SPN-4 in vitro. In a genetic screen to identify factors that work with SPN-4, we isolated mutant alleles of CCR4-NOT components. Auxin-induced degradation of the LET-711/NOT1 scaffold and the CCF-1 deadenylase disrupted clearance of two SPN-4-associated transcripts. Our results support a model in which SPN-4 initiates expression in late-stage oocytes, associates with maternal mRNA targets through RNA sequences in their 3UTRs and promotes CCR4-NOT-mediated decay during early embryogenesis.

developmental biology↗

bioRxiv2025

Genome compartmentalization in a host-specific fungal insect pathogen reveals a putative mating type locus on an accessory chromosome

The genomic diversity of many fungal pathogens is driven by rapidly evolving regions harbouring significant amounts of transposable elements. Such genomic regions often contain genes important for pathogenicity and may be sequestered from the core genome on accessory chromosomes, which are variably present in isolates of a species. In this study, we present a pangenomic analysis of a fungal insect pathogen, Metarhizium acridum, using seven chromosome-scale genomes from four different continents. We show that approximately 25% of the M. acridum pangenome is comprised of genes only present in one isolate (singletons) or more than one but not all isolates (accessory). These genes are enriched for functions in secondary metabolite production, nutrient transport, and chromosome organization. We also find evidence of functional compartmentalization of the genome, as the core genome of M. acridum is enriched in carbohydrate-active enzymes, while the accessory components are enriched in effectors that are located in gene-sparse regions of the genome. Furthermore, we identified the first naturally recovered accessory chromosome in M. acridum, which does not harbor effector or secondary metabolite proteins related to host-insect interactions but is enriched in functions related to sexual reproduction. Within the genus Metarhizium, M. acridum is one of few species considered to regularly reproduce sexually. We show that the accessory chromosome contains genes from both the MAT1-1 and MAT1-2 idiomorphs, in addition to the MAT locus found on the core chromosomes. Our findings suggest that the presence of this accessory chromosome may facilitate sexual reproduction, possibly even primary homothallism, in the otherwise heterothallic M. acridum. Overall, our study presents a putative novel mechanism whereby this fungal pathogen may acquire gene recombination and ensure maintenance of the accessory chromosome.

microbiology↗

bioRxiv2023

NODDI-derived measures of microstructural integrity in medial temporal lobe white matter pathways are associated with Alzheimer's disease pathology and cognitive outcomes

INTRODUCTIONDiffusion tensor imaging has been used to assess white matter (WM) changes in the early stages of Alzheimers disease (AD). However, the tensor model is necessarily limited by its assumptions. Neurite Orientation Dispersion and Density Imaging (NODDI) can offer insights into microstructural features of WM change. We assessed whether NODDI more sensitively detects AD-related changes in medial temporal lobe WM than traditional tensor metrics. METHODSStandard diffusion and NODDI metrics were calculated for medial temporal WM tracts from 199 older adults drawn from ADNI3 who also received PET to measure pathology and neuropsychological testing. RESULTSNODDI measures in medial temporal tracts were more strongly correlated to cognitive performance and pathology than standard measures. The combination of NODDI and standard metrics exhibited the strongest prediction of cognitive performance in random forest analyses. CONCLUSIONSNODDI metrics offer additional insights into contributions of WM degeneration to cognitive outcomes in the aging brain.

neuroscience↗

bioRxiv2022

Translation of the ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo

mRNA localization and transport are integral in regulating gene expression. In Caenorhabditis elegans embryos, the maternally inherited mRNA erm-1 (Ezrin/Radixin/Moesin) concentrates in anterior blastomeres. erm-1 mRNA localizes within those blastomeres to the plasma membrane where the essential ERM-1 protein, a membrane-actin linker, is also found. We demonstrate that the localization of erm-1 mRNA to the plasma membrane is translation-dependent and requires its encoded N-terminal membrane-binding (FERM) domain. By perturbing translation through multiple methods, we found erm-1 mRNA localization at the plasma membrane was maintained only if the nascent peptide remained in complex with the translating mRNA. Indeed, recoding the erm-1 mRNA coding sequence while preserving the encoded amino acid sequence did not disrupt erm-1 mRNA localization, corroborating that the information directing mRNA localization resides within its membrane-binding protein domain. A smiFISH screen of 17 genes encoding similar membrane-binding domains identified three plasma membrane localized mRNAs in the early embryo. Nine additional transcripts showed apparent membrane localization later in development. These findings point to a translation-dependent pathway for localization of mRNAs encoding membrane-associated proteins. SUMMARY STATEMENTIn C. elegans, erm-1 mRNA localization to plasma membranes requires translation of the ERM-1 membrane-binding domain

developmental biology↗

bioRxiv2021

Improved methods for protein and single-molecule RNA detection in C. elegans embryos

Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule Fluorescence In Situ Hybridization (smFISH) and Immunofluorescence (IF) visualize the abundance and localization of mRNAs and proteins, respectively, allowing researchers to elucidate the localization, dynamics, and functions of many genes. Here, we describe several improvements and optimizations to existing IF and smFISH approaches specifically for use in C. elegans embryos. We present 1) optimized fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility, 2) a streamlined, in-tube approach that negates freeze-cracking, 3) the smiFISH (single molecule inexpensive FISH) adaptation that reduces cost, 4) an assessment of optimal anti-fade products, and 5) straightforward quantification and data analysis methods. Most importantly, published IF and smFISH protocols have predominantly been mutually exclusive, preventing exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we present methods to combine IF and smFISH protocols in C. elegans embryos including an efficient method harnessing nanobodies. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol.

cell biology↗

bioRxiv2021

Substantial Differences in SARS-CoV-2 Antibody Responses Elicited by Natural Infection and mRNA Vaccination

We analyzed data from two ongoing COVID-19 longitudinal serological surveys in Orange County, CA., between April 2020 and March 2021. A total of 8,476 finger stick blood specimens were collected before and after an aggressive mRNA vaccination campaign. IgG levels were determined using a multiplex antigen microarray containing 10 SARS-CoV-2 antigens, 4 SARS, 3 MERS, 12 Common CoV, and 8 Influenza antigens. Twenty-six percent of 3,347 specimens from unvaccinated Orange County residents in December 2020 were SARS-CoV-2 seropositive. The Ab response was predominantly against nucleocapsid (NP), full length spike and the spike S2 domain. Anti-receptor binding domain (RBD) reactivity was low and there was no cross-reactivity against SARS S1 or SARS RBD. An aggressive mRNA vaccination campaign at the UCI Medical Center started on December 16, 2020 and 6,724 healthcare workers were vaccinated within 3 weeks. Seroprevalence increased from 13% in December to 79% in January, 93% in February and 99% in March. mRNA vaccination induced much higher Ab levels especially against the RBD domain and significant cross-reactivity against SARS RBD and S1 was also observed. Nucleocapsid protein Abs can be used to distinguish individuals in a population of vaccinees to classify those who have been previously infected and those who have not, because nucleocapsid is not in the vaccine. Previously infected individuals developed higher Ab titers to the vaccine than those who have not been previously exposed. These results indicate that mRNA vaccination rapidly induces a much stronger and broader Ab response than SARS-CoV-2 infection.

immunology↗

bioRxiv2021

Antimalarial mass drug administration in large populations and the evolution of drug resistance

Mass drug administration (MDA) with antimalarials has been shown to reduce prevalence and interrupt transmission in small populations, in populations with reliable access to antimalarial drugs, and in populations where sustained improvements in diagnosis and treatment are possible. Effective MDA eliminates drug-resistant parasites which has the long-term benefit of extending the useful therapeutic life of first-line therapies for all populations, not just the focal population where MDA was carried out. However, in order to plan elimination measures effectively, it is necessary to characterize the conditions under which failed MDA could exacerbate resistance. We use an individual-based stochastic model of Plasmodium falciparum transmission to evaluate this risk in large populations (>40K) where access to antimalarial treatments may not be uniformly high and where re-importation of drug-resistant parasites may be common. We find that drug-resistance evolution can be accelerated by MDA when all three of the following conditions are met: (1) strong genetic bottlenecking that falls short of elimination, (2) re-importation of resistant genotypes, and (3) continued selection pressure during routine case management post-MDA. Accelerated resistance levels are not immediate but follow the rebound of malaria cases post-MDA, if this is allowed to occur. Crucially, resistance is driven by the selection pressure during routine case management post-MDA and not the selection pressure exerted during the MDA itself. Second, we find that increasing treatment coverage post-MDA increases the probability of local elimination in low-transmission regions (PfPR < 2%) in scenarios with both low and high levels of drug-resistance importation. This emphasizes the importance of preparation and planning to ensure that MDA has a high probability of leading to elimination, and the necessity of supporting public health infrastructure to provide high coverage of diagnosis and treatment post-MDA.

evolutionary biology↗

bioRxiv2020

Epidemiology of Dengue viral infection in Nepal: 2006-2019

BackgroundDengue is one of the newest emerging diseases in Nepal with increasing burden and geographic spread over the last 14 years. The main objective of this study was to explore the spatio-temporal epidemiological patterns of Dengue since its first report (2006) till 2019 in Nepal. MethodsThis study is a retrospective analysis of dengue data available from the Epidemiological Disease Control Division (EDCD) of Government of Nepal. The data in this study cover the last 14 years (2006-2019) of reported dengue cases in Nepal. Epidemiological trend and spatio-temporal analyses were performed. Maps of reported case incidence were created using QGIS version 3.4. ResultsSince the first report of dengue in a foreigner in 2004, Nepal reported a total of 17,992 dengue cases in 68 districts of Nepal in 2019. The incidence was approximately five times higher in 2018 (Incidence Rate Ratio (IRR): 4.8; 95% CI: 1.5 - 15.3) and over 140 times higher in 2019 (IRR: 141.6; CI: 45.8 - 438.4). Population density was not a statistically significant predictor of case incidence. Mean elevation had a negative association with case incidence. A one standard deviation increase in elevation was associated with a 90% decrease in reported case incidence (IRR: 0.10; CI: 0.01 - 0.20). However, the association with mean elevation varied across the years. In comparison to 2016, incidence was greater at higher elevations in 2018 (IRR: 22.7; CI: 6.0 - 86.1) and 2019 (IRR: 9.6; CI: 2.6 - 36.1). ConclusionThere is a high risk of dengue outbreak in the Terai region with increasing spread towards the mid-mountains and beyond as seen over the last 14 years. Urgent measures are required to increase the availability of diagnostics and resources to mitigate future dengue epidemics. Findings from this study can inform the spatio-temporal distribution of dengue and can help in resource allocation and priority setting for future epidemic. Author summaryDengue in humans is caused by four different serotypes (DENV-1, DENV-2, DENV-3 & DENV-4). Globally it is the most pervasive vector borne diseases with increasing number of cases in recent years. Dengue is one of the youngest emerging diseases in Nepal with increasing cases and spread from the tropical lowland to the highland (hilly) regions. We conducted a spatio-temporal analysis of national data to consolidate the information using QGIS to measure the dengue incidence at district levels of Nepal. Spatio-temporal analysis exploring the incidence and distribution of dengue cases aids in identification of high-risk areas which can ultimately enable national dengue programme to mobilize and allocate resources for the control and treatment. This study shows, the persistent high risk of dengue outbreak in lowland Terai region with annual rise in the risk of spread towards the mid-mountains and beyond. Urgent measures are required to increase the diagnostics and resources to mitigate the epidemic burden of dengue in Terai and peripheral regions.

microbiology↗

bioRxiv2020

mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage

Caenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription. This presents an opportunity to study mechanisms of post-transcriptional regulatory control. In seeking the mechanisms behind this patterning, we discovered that some cell-specific mRNAs accumulate non-homogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage), and P-bodies (associated with RNA processing). Transcripts differed in their dependence on 3UTRs and RNA Binding Proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling these, we untangled a long-standing question: Are mRNAs directed to P granules for translational repression or do they accumulate there as a downstream step? We found translational repression preceded P granule localization and could occur independent of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. Overall, we show transcripts important for germline development are directed to P granules by translational repression, and this, in turn, directs their accumulation in the progenitor germ lineage where their repression can ultimately be relieved. SummaryMaternally loaded mRNAs localize non-homogeneously within C. elegans early embryos correlating with their translational status and lineage-specific fates.

developmental biology↗

bioRxiv2018

Herd protection against Plasmodium falciparum infections conferred by mass antimalarial drug administrations and the implications for malaria elimination

IntroductionAll nations of the Greater Mekong Subregion have committed to elimination of malaria by the year 2030. Elimination efforts rely on increasing access to diagnosis and treatment. However, asymptomatic infections pose a major challenge for these efforts. One approach towards eliminating asymptomatic reservoirs is targeted mass antimalarial drug administration (MDA). Here we present a fine scale spatiotemporal analysis of malaria incidence and prevalence in villages undergoing MDA.\n\nMethodsFour villages along the Myanmar-Thailand border were selected for a MDA pilot study based on clinical records and prevalence surveys. Passive detection of clinical episodes was facilitated through community based malaria clinics in each village. All villagers were screened using venous blood and ultra-sensitive qPCR (uPCR) for detection of parasites at baseline and every subsequent 3 months until month 18 (M18). A final screening was done at M24. MDAs were conducted on M0, M1 and M2 in two villages and on M9, M10, M11 in the remaining two villages. Which villages received early or deferred MDA was decided using restricted randomization. MDA participation, clinical episodes and uPCR detected infections were mapped to participant houses. Scan statistics were used to test for clusters of malaria episodes, malaria infections and non-adherence to MDA. Mixed effects regressions were used to test for risk factors for clinical episodes after MDA.\n\nResultsNeighborhood level MDA adherence was a major predictor for clinical episodes of malaria post-MDA, suggesting a strong herd effect. Each village had a cluster of P. falciparum infections at M0. After M0, there were no clusters of uPCR detectable P. falciparum infections. Clinical episodes of P. falciparum occurred in one village only which had a cluster of non-adherence to MDA and a high mosquito vector human biting rate. Individuals with subclinical P.falciparum infections were more likely to have subsequent clinical episodes than individuals who had no subclinical infections. Individuals who lived in a house with someone who had a clinical episode were more likely to also have a clinical episode subsequently than individuals residing in a house free of P.falciparum infections.\n\nConclusionTo our knowledge this is the first study to show a herd effect from MDA for malaria. These data and results have significance for spatial targeting of interventions for malaria elimination. Clusters of non-adherence to MDA participation can lead to failed elimination if they occur among individuals with asymptomatic infections and given sufficient mosquito vector exposure. Community participation, which can be facilitated through community engagement, is key to MDA success.

epidemiology↗

bioRxiv2017

Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea)

With an estimated population size of less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) has been listed as near threatened by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which could provide valuable insights about its evolutionary history and aid in conservation efforts of the species. Here we report both mitochondrial and nuclear genomes of wild-caught brown hyena individuals from across southern Africa. Mitochondrial DNA shows little to no phylogeographic structure, whereas low-coverage nuclear genomes reveal several potential sub-populations. Moreover, we find that brown hyenas harbour the lowest genetic diversity for a species on both the mitochondrial and nuclear level when compared to a number of mammalian species for which such information is currently available. Our data also reveal that at least on the nuclear DNA level, this low diversity could be the result of a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. Moreover, our findings also show that the correlation between genetic diversity and the perceived risk of extinction is not particularly strong, since many species with higher genetic diversity than the brown hyena are considered to be at greater risk of extinction. Taken together, our results have important implications for the conservation status and conservation approaches of the brown hyena.

evolutionary biology↗