Biology subjects

Kelley, K.

Publications and source records attributed to Kelley, K..

10 recordsLinked to original sources

bioRxiv2026

Genotypic evidence of vector-mediated selection on Plasmodium falciparum in infected field-collected Anopheles mosquitoes

Malaria-causing Plasmodium parasites are transmitted between vertebrate hosts via diverse species of Anopheles mosquitoes. The P47 protein in Plasmodium falciparum has been shown to affect transmission in various anopheline species by mediating evasion of mosquito innate immunity in an allele-specific manner. The Pfs47 gene that encodes P47 exhibits high genetic divergence across continents, as well as high genetic diversity within many parasite populations, but the impact of polymorphisms on transmission success in different sympatric vectors has not been previously studied in a field context. Here we report parasite genotyping data from naturally infected, field-collected mosquitoes at sites harboring at least two prevalent sympatric vector species, targeting Pfs47 in addition to the CSP, AMA1, SERA2, and TRAP parasite antigens. Collections took place at Ndangueng, Cameroon and Benguia, Gabon between November 2019 and July 2021, yielding infected Anopheles gambiae at both sites in addition to Anopheles moucheti in Cameroon and Anopheles funestus in Gabon. We found no significant difference in the mean number of parasite strains in infected sympatric mosquito species from each site. However, Pfs47 exhibited a significant difference in the prevalence of an amino acid polymorphism (I248L) between An. moucheti and An. gambiae in Cameroon. Polymorphisms at two additional positions (N272Y/I and P369H) displayed significant linkage disequilibrium with I248L, and there were significant differences in the distribution of Pfs47 haplotypes between sympatric mosquito species at both sites. These findings demonstrate divergent selection on P. falciparum mediated by sympatric vector species, suggesting that parasite genotype significantly impacts local vectorial capacity by modulating species-specific vector competence.

evolutionary biology↗

bioRxiv2025

Subtle Cellular Phenotypes Inform Pathological and Benign Genetic Mutants in the Iduronidase-2 Sulfatase Gene

As with most enzyme-storage disorders, DNA testing at an early age is critical for identifying genetic variants and their impact on disease burden. Still, most variants in genes such as Iduronate-2-sulfatase, IDS, are Variants of Uncertain Significance (VUS). In patients presenting with Hunter Syndrome, clinical testing for IDS enzyme activity has been the mainstay to determine whether a variant is likely damaging. However, these enzyme assays are unable to predict disease severity or neuronal toxicity and may be missing many aspects of IDS pathology. In this study, we have developed an image-based assay using genome-engineered cells with IDS mutations to identify if a specific mutation causes lysosomal and membrane disruptions that characterize the disease. Specifically, we generate twelve mutant cell lines and document both the biochemical changes in IDS activity and the reproducible phenotypic differences therein. Next, we examine two patient-derived cell lines and find the same phenotypic differences in these lines compared to parental controls. The phenotypic changes are measured on a specific scale, which we term the PathScoreLC. To determine whether the observed changes are specific to IDS, we reintroduce a recombinant version of the IDS enzyme (rhIDS) to rescue both the biochemical and phenotypic changes of these cells. Interestingly, even after 120 hours, rescue is present, but not all the cells return to normal, which may also reflect the pathological state. Finally, we examine the gene expression differences and find that recombinant enzyme is not sufficient to induce transcriptional changes in the mutant lines at the time points studied. Overall, these cell-based lysosomal and membrane phenotypes may be key to quickly and accurately profiling clinical variants in the IDS gene.

cell biology↗

bioRxiv2024

Experience instructs the refinement of feature-selectivity in the mouse primary visual thalamus

Neurons exhibit selectivity for specific features: a property essential for extracting and encoding relevant information in the environment. This feature-selectivity is thought to be modifiable by experience at the level of the cortex. Here, we demonstrate that selective exposure to a feature during development can instruct the population representation for that feature in the primary visual thalamus. This thalamic plasticity is not simply inherited from the cortex because it is still observed when recordings were performed in the absence of cortical feedback. Moreover, plasticity is blocked in mutant mice that exhibit deficits in retinogeniculate refinement, indicating that alterations in feature-selectivity are a direct result of changes in feedforward connectivity. These experience-dependent changes persist into older ages--highlighting the importance of this developmental period in shaping population coding in the thalamus. Our results show that salient environmental features are hard-wired into thalamic circuits during a discrete developmental window.

neuroscience↗

bioRxiv2024

Children Who Develop Celiac Disease Exhibit Distinct Metabolic Pathways Among Their Gut Microbiota Years Before Diagnosis

Celiac disease (CD) is an autoimmune condition caused by a loss of tolerance to gluten in genetically predisposed individuals. While 30-40% of people possess the predisposing alleles, only 1-2% of the population is diagnosed with CD. This indicates environmental factors play a role in the pathogenesis of the disease, however the trigger of gluten tolerance loss is unknown. The gut microbiome composition of CD patients differs in comparison to their healthy counterparts; however, a causal link has not been established. In this study, we examined the alterations in the composition of the gut microbiota in a retrospective, longitudinal cohort of 10 children at age 1, matched for sex, human leukocyte antigen (HLA) genotype and breastfeeding duration. All samples were obtained from the pediatric donors prior to diagnosis (CD progressors). We used Ig-A sequencing combined with 16S sequencing for samples obtained at age 1. We also identified the functional metabolic pathways enriched in CD progressors compared to the healthy controls at ages 1, 2.5 (n=15-16) and 5 (n=9-13) using data from a similar study that we previously completed. Our findings demonstrate that CD progressors have ASV-level alterations in their gut microbiome as early as the first year of life, including the increased presence of some taxa that have been previously been reported to be enriched in CD. Using PICRUSt analysis, we also showed that inflammatory- and pathogenicity-related functions are enriched in CD progressors gut microbiome years before diagnosis. These pathways include glycine, serine and threonine metabolism, N-glycan biosynthesis and fatty acid biosynthesis and beta-lactam resistance, which are potentially contributing to chronic inflammation in CD. Overall, our results indicate distinct metabolic pathways enriched in the gut microbiome of CD progressors years before diagnosis. Understanding these pathways could advance our understanding of CD pathogenesis and its link to the gut microbiome.

microbiology↗

bioRxiv2023

Prostaglandins as Candidate Ligands for a Per-ARNT-Sim (PAS) Domain of Steroid Receptor Coactivator 1 (SRC1)

Steroid receptor coactivators (SRCs) comprise a family of three paralogous proteins commonly recruited by eukaryotic transcription factors. Each SRC harbors two tandem Per-ARNT-Sim (PAS) domains that are broadly distributed that bind small molecules and regulate interactions. Using computational docking, solution NMR, mass spectrometry, and molecular dynamics simulations, we show that the SRC1 PAS-B domain can bind to certain prostaglandins (PGs) either non-covalently to a surface that overlaps with the site used to engage transcription factors or covalently to a single, specific, conserved cysteine residue next to a solvent accessible hydrophobic pocket. This pocket is in proximity to the canonical transcription factor binding site, but on the opposite side of the domain, suggesting a potential mode of regulating transcriptional activator-coactivator interactions.

biochemistry↗

bioRxiv2023

Targeted and selective knockout of the TLQP-21 neuropeptide unmasks its unique role in energy homeostasis

Pro-peptide precursors are processed into biologically active peptide hormones or neurotransmitters, each playing an essential role in physiology and disease. Genetic loss of function of a pro-peptide precursor results in the simultaneous ablation of all biologically-active peptides within that precursor, often leading to a composite phenotype that can be difficult to align with the loss of specific peptide components. Due to this biological constraint and technical limitations, mice carrying the selective ablation of individual peptides encoded by pro-peptide precursor genes, while leaving the other peptides unaffected, have remained largely unaddressed. Here, we developed and characterized a mouse model carrying the selective knockout of the TLQP-21 neuropeptide ({Delta}TLQP-21) encoded by the Vgf gene. To achieve this goal, we used a knowledge-based approach by mutating a codon in the Vgf sequence leading to the substitution of the C-terminal Arginine of TLQP-21, which is the pharmacophore as well as an essential cleavage site from its precursor, into Alanine (R21[->]A). We provide several independent validations of this mouse, including a novel in-gel digestion targeted mass spectrometry identification of the unnatural mutant sequence, exclusive to the mutant mouse. {Delta}TLQP-21 mice do not manifest gross behavioral and metabolic abnormalities and reproduce well, yet they have a unique metabolic phenotype characterized by a temperature-dependent resistance to diet-induced obesity and activation of the brown adipose tissue.

physiology↗

bioRxiv2021

Neurotrophic control of size regulation during axolotl limb regeneration

The mechanisms that regulate the sizing of the regenerating limb in tetrapods such as the Mexican axolotl are unknown. Upon the completion of the developmental stages of regeneration, when the regenerative organ known as the blastema completes patterning and differentiation, the limb regenerate is proportionally small in size. It then undergoes a phase of regeneration that we have called the "tiny-limb" stage, that is defined by rapid growth until the regenerate reaches the proportionally appropriate size. In the current study we have characterized this growth and have found that signaling from the limb nerves is required for its maintenance. Using the regenerative assay known as the Accessory Limb Model, we have found that the size of the limb can be positively and negatively manipulated by nerve abundance. We have additionally developed a new regenerative assay called the Neural Modified-ALM (NM-ALM), which decouples the source of the nerve from the regenerating host environment. Using the NM-ALM we discovered that non-neural extrinsic factors from differently sized host animals do not play a prominent role in determining the size of the regenerating limb. We have also discovered that the regulation of limb size is not autonomously regulated by the limb nerves. Together, these observations show that the limb nerves provide essential and instructive cues to regulate the final size of the regenerating limb.

developmental biology↗

bioRxiv2020

Waffle method: A general and flexible approach for FIB-milling small and anisotropically oriented samples

Cryo-FIB/SEM combined with cryo-ET has emerged from within the field of cryo-EM as the method for obtaining the highest resolution structural information of complex biological samples in-situ in native and non-native environments. However, challenges remain in conventional cryo-FIB/SEM workflows, including milling thick specimens that do not vitrify well, specimens with preferred orientation, low-throughput when milling small and/or low concentration specimens, and cellular specimens that distribute poorly across grid squares. Here we present a general approach we call the Waffle Method which leverages high-pressure freezing to address these challenges. We illustrate the mitigation of these challenges by applying the Waffle Method and cryo-ET to reveal the macrostructure of the polar tube in microsporidian spores in multiple complementary orientations, which was previously not possible due to preferred orientation of the spores on the grid. We demonstrate the broadness of the Waffle Method by applying it to three additional cellular samples and a single particle sample using a variety of cryo-FIB-milling hardware, with both manual and automated approaches. We also present a unique and critical stress-relief gap designed specifically for waffled lamellae. Additionally, we describe applications of the Waffle Method which are currently being explored. We propose the Waffle Method as a way to achieve many of the advantages of cryo-liftout on the specimen grid while avoiding the long, challenging, and technically-demanding process required for cryo-liftout.

microbiology↗

bioRxiv2018

The impact of data reduction and lossy image formats on electron microscope images

Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. Coupled with the adoption of automated pipelines, significant infrastructure support is required to sustain high throughput workflows. In particular, data generation rates may outpace the ability to deploy data storage and archival solutions. We have investigated what effects data compression and conversion to different file formats have on the ability to obtain high resolution cryoEM reconstructions. Standard lossless data compression strategies have a high impact on reducing the size of direct detector electron counting movie stacks, but provide more modest gains for aligned summed images. We show that EM images can be compressed using standard lossy methods to reduce file storage to 5-10% of the size of the original aligned sum or movie stack file and yet still retain enough information such that modern image processing pipelines will provide sub-2[A] reconstructions from the compressed data.

biophysics↗

bioRxiv2017

MicroRNA-451a regulates colorectal cancer radiosensitivity

Colorectal cancer (CRC) is a leading cause of cancer-related death. The responses of CRC to standard of care adjuvant therapies such as radiation or chemotherapy are poorly understood. MicroRNAs (miRs) are small non-coding RNAs that affect gene expression programs in cells by downregulating specific mRNAs. In this study, we discovered a set of microRNAs upregulated rapidly in response to a single 2 Gy dose fraction of {gamma}-radiation in a mouse colorectal carcinoma xenograft model. The most upregulated candidate in our signature, miR-451a inhibits tumor cell proliferation and attenuated surviving fraction in longer-term cultures. Conversely, inhibition of miR-451a increased proliferation, tumorsphere formation and surviving fraction of tumor cells. Using a bioinformatics approach, we identified four genes-CAB39, EMSY, MEX3C and EREG as targets of miR-451a. Transfection of miR-451a decreased both mRNA and protein levels of these targets. Importantly, we found miR-451a expression was decreased with tumor stage in a small subset of CRC patients. Finally, analysis of a TCGA colorectal cancer dataset reveals that the CAB39 and EMSY are upregulated at the protein level in a significant number of CRC patients and correlates with poorer overall survival. Taken together, our data indicates miR-451a influences the radiation sensitivity of colorectal carcinomas.

cancer biology↗