Biology subjects

Williams, C. L.

Publications and source records attributed to Williams, C. L..

16 recordsLinked to original sources

bioRxiv2026

Alkamines reveal a hidden layer of steroid and drug metabolism

Biomedical research overlooks most genes in favor of a well-studied minority, yet whether analogous blind spots exist in metabolomics remains unknown. We show that reductive amination, forming secondary amines from aldehydes or ketones and amines, generates a previously hidden class of metabolites we term alkamines. Multiplexed synthesis of 8,475 alkamines combined with MS/MS searches across 1.7 billion spectra identified 1,626 candidates across multiple species and organs. Of these, 56 were confirmed in biological samples, including 27 steroid- and 12 drug-derived alkamines matching prescription patterns. Notably, 77% of synthesized alkamines are absent from PubChem. This combinatorial logic likely explains why alkamines have evaded detection and suggests drug metabolism frameworks substantially underestimate drug-derived metabolite diversity. Reductive amination is an overlooked route modifying steroids, bile acids, and xenobiotics.

biochemistry↗

bioRxiv2025

Uncovering the Genomic Landscape of Mycobacterium bovis in Wales

Bovine tuberculosis (bTB), caused by the bacterium Mycobacterium bovis, is one of the most pressing animal health issues in Wales today. It negatively impacts cattle health, affects profitability and trade, and can decimate years of genetic improvement towards desirable production traits. It also places a significant burden on the health and well-being of affected farming families. Eradication of bTB requires the understanding of local transmission pathways to target effective disease control interventions. Traditional genotyping methods, such as spoligotyping and VNTR analysis, which have previously been used in Wales to understand the epidemiology of M. bovis, have lacked the discriminatory power to accurately identify local transmission pathways. Recently, whole-genome sequencing has replaced traditional genotyping methods for all M. bovis strains isolated from infected animals in Wales. In this study, we characterised the genomic diversity of M. bovis across Wales by analysing the genome sequence of all 379 M. bovis isolates obtained from culture-positive animals in Wales in 2021. Analyses uncovered three main clusters that are geographically distinct. A further three clusters containing fewer isolates were also geographically separated, two of which had particularly large SNP distances compared to the majority of other Welsh isolates, suggesting independent introductions of M. bovis strains that are not endemic to Wales. Fine-scale and epidemiologically relevant genetic structuring was identified within the six main clusters, indicating region-specific evolution, which can drive local disease dynamics. Finally, A number of SNPs in coding genes were identified that have the potential for important advantageous physiological consequences that may impact host-pathogen interactions and necessitate further investigation.

microbiology↗

bioRxiv2025

Neuroimaging Biomarkers of Neuroprotection: Impact of Voluntary versus Enforced Exercise in Alzheimers Disease Models

Exercise is a promising strategy for preventing or delaying Alzheimers disease (AD), yet its mechanisms remain unclear. We investigated how exercise influences brain structure, function, and behavior in a familial AD model. Mice underwent voluntary, voluntary plus enforced exercise, or remained sedentary. Neuroimaging included in vivo manganese-enhanced MRI (MEMRI). perfusion, and ex vivo diffusion MRI to assess morphometry, activity, cerebral blood flow (CBF), microstructural integrity and connectivity. Both exercise regimens induced structural and functional brain adaptations while reducing anhedonia. Voluntary exercise increased cortical and limbic volumes, particularly in the hippocampus, cingulate, and entorhinal cortex, supporting cognitive and emotional regulation. Adding enforced exercise influenced subcortical and sensory regions, including visual, motor and associative areas, supporting sensory-motor integration. MEMRI revealed increased activity in sensorimotor, limbic, and associative cortices, with voluntary exercise enhancing limbic and associative regions, and enforced exercise strengthening sensorimotor and subcortical circuits. White matter integrity improved in memory-associate pathways such as the corpus callosum, cingulum, and hippocampal commissure. Synaptic remodeling was observed in the cingulate cortex, anterior thalamic nuclei, and amygdala. Voluntary exercise enhanced CBF in the motor cortex and hippocampus, while enforced exercise limited these increases. Connectivity analyses revealed exercise-responsive networks spanning the cingulate cortex, entorhinal cortex, anterior thalamic nuclei, and basolateral amygdala, and associated tracts. Graph analyses linked running distance with increased thalamic, brainstem, and cerebellar connectivity, associating exercise intensity with plasticity. These findings highlight the ability of chronic exercise to modulate neuroimaging biomarkers through distinct but complementary pathways, reinforcing its potential as a neuroprotective intervention for AD. HighlightsO_LIExercise alters MRI biomarkers via distinct and partially overlapping mechanisms. C_LIO_LIVoluntary exercise boosts cortical and limbic regions for emotion and cognition. C_LIO_LIEnforced exercise strengthens subcortical and sensory areas for motor control. C_LIO_LIFA increases suggest memory tract reinforcement and grey matter remodelling. C_LIO_LIGraph analysis reveals plasticity in memory, emotion, and reward circuits. C_LI

neuroscience↗

bioRxiv2024

RPS19 and RPL5, the most commonly mutated genes in Diamond Blackfan anemia, impact DNA double-strand break repair

Diamond Blackfan anemia (DBA) is caused by germline heterozygous loss-of-function pathogenic variants (PVs) in ribosomal protein (RP) genes, most commonly RPS19 and RPL5. In addition to red cell aplasia, individuals with DBA are at increased risk of various cancers. Importantly, the mechanism(s) underlying cancer predisposition are poorly understood. We found that DBA patient-derived lymphoblastoid cells had persistent {gamma}-H2AX foci following ionizing radiation (IR) treatment, suggesting DNA double-strand break (DSB) repair defects. RPS19- and RPL5-knocked down (KD) CD34+ cells had delayed repair of IR-induced DSBs, further implicating these RPs in DSB repair. Assessing the impact of RPS19- and RPL5-KD on specific DSB repair pathways, we found RPS19-KD decreased the efficiency of pathways requiring extensive end-resection, whereas RPL5-KD increased end-joining pathways. Additionally, RAD51 was reduced in RPS19- and RPL5-KD and RPS19- and RPL5-mutated DBA cells, whereas RPS19-deficient cells also had a reduction in PARP1 and BRCA2 proteins. RPS19-KD cells had an increase in nuclear RPA2 and a decrease in nuclear RAD51 foci post-IR, reflective of alterations in early, critical steps of homologous recombination. Notably, RPS19 and RPL5 interacted with poly(ADP)-ribose chains noncovalently, were recruited to DSBs in a poly(ADP)-ribose polymerase activity-dependent manner, and interacted with Ku70 and histone H2A. RPL5s recruitment, but not RPS19s, also required p53, suggesting that RPS19 and RPL5 directly participate in DSB repair via different pathways. We propose that defective DSB repair arising from haploinsufficiency of these RPs may underline the cancer predisposition in DBA. KEY POINTSO_LIRPS19- and RPL5-deficiency alters DNA double-strand break repair, which may underlie cancer predisposition in Diamond Blackfan anemia. C_LIO_LIRPS19 and RPL5 bind PAR chains and are rapidly recruited to sites of DNA double-strand breaks, suggesting active roles in repair. C_LI

molecular biology↗

bioRxiv2024

Parent attention-orienting behavior is associated with neural entropy in infancy

Parents play a significant role in directing infants attention to environmental stimuli via joint attention. We hypothesized that infants whose parents provide more bids for joint attention will display a more complex neural response when viewing social scenes. Sixty-one 8-month-old infants underwent electroencephalography (EEG) while viewing videos of joint-and parallel-play and participated in a parent-infant free play interaction. EEG data was analyzed using multiscale entropy, which quantifies moment-to-moment neural variability. Free play interactions were coded for parent alternating gaze, a behavioral mechanism for directing attention to environmental cues. We found a significant positive association between parent alternating gaze and neural entropy in frontal and central brain regions. These results suggest a relationship between parent behavior and infant neural mechanisms that regulate social attention, underlying the importance of parent cues in the formation of neural networks in infancy.

neuroscience↗

bioRxiv2023

Environmental change drives multi-generational shifts in the gut microbiome that mirror changing animal fitness

Gut microbiomes can dramatically affect host health and fitness and can also be highly dynamic in response to changing environmental conditions. This intricate interplay between gut microbiota, environmental pressures, and host health necessitates accounting for all these variables when predicting the response of animals to a changing environment. These predictions are of broad concern but are highly relevant to conservation biology, and more specifically to populations transitioning from the wild to human care for the purposes of ex situ breeding programs. Captivity can dramatically alter both host-associated microbial communities and host health, but the dynamics of how the host and microbiome transition between the wild and captive state--within and across generations--are not well described. Here, we evaluate the microbiome and host fitness metrics for Pacific pocket mice (Perognathus longimembris pacificus) during the establishment of an ex situ conservation breeding program to characterize how pocket mice and their microbiomes respond to the environmental pressures of captivity across five generations. We found that the microbiome assumes a novel, stable conformation after two to three generations in captivity and that the patterns observed in the transitioning microbiota mirror the patterns of transitioning hosts weight and reproductive metrics. Moreover, we identify several microbial taxa which are correlated with successful reproduction. Our results provide insight not only into the effects of captivity but can be broadly applicable for understanding the effects of environmental change on organisms and their gut microbiota, which we propose may require multiple generations to reach an alternative stable state.

ecology↗

bioRxiv2023

Hyperextended telomeres promote C-circle formation in telomerase positive human cells

Telomere length maintenance is crucial to cancer cell immortality. Up to 15% of cancers utilize a telomerase-independent, recombination-based mechanism termed alternative lengthening of telomeres (ALT). The primary ALT biomarker is the C-circle, a type of circular DNA with extrachromosomal telomere repeats (cECTRs). How C-circles form is not well characterized. To investigate C-circle formation in telomerase+ cells, we studied the human cen3tel cell line, in which telomeres progressively hyper-elongated post TERT-immortalization. cECTR signal was observed in 2D gels and C-circle assays but not t-circle assays, which also detect cECTRs. Telomerase activity and C-circle signal were not separable in the analysis of clonal populations, consistent with C-circle production occurring within telomerase+ cells. Two other long telomere, telomerase+ (LTT+) cell lines, HeLa1.3 (~23 kb telomeres) and HeLaE1 (~50 kb telomeres), had similar cECTR properties. Telomerase activity did not directly impact C-circle signal in LTT+ cells; instead, C-circle signal correlated with telomere length. LTT+ lines were less sensitive to hydroxyurea than an ALT+ cell line, suggesting that ALT status is a stronger contributor to replication stress levels than telomere length. Additionally, FANCM did not suppress C-circles in LTT+ cells as it does in ALT+ cells. Thus, C-circle formation may be driven by telomere length, independently of telomerase and replication stress, highlighting limitations of C-circles as a stand-alone ALT biomarker.

cancer biology↗

bioRxiv2023

Maternal diesel exposure and maternal choline supplementation interactions in fetal and placental immune factors

Air pollution causes widespread inflammatory changes in the body and brain. When exposure to air pollution occurs early in development, children exhibit impaired working memory ability (Sunyer et al., 2015). In addition, prenatal exposure to diesel particulate matter (DEP) increases inflammatory cytokine expression in the whole brain of embryonic day 18 (E18) males and leads to adverse long-term negative outcomes (Bolton et al., 2012). In contrast, dietary choline supplementation is negatively correlated with inflammatory cytokine production in adult rats and cultured human cells (Zhang et al., 2018; Jiang et al., 2014). When administered as a supplement to pregnant rats, choline also improves working memory in adulthood (Meck et al., 2008; Meck & Williams, 1999; 1997). The current study sought to determine if prenatal dietary choline supplementation protects against the effects of air pollution in the developing brain and in the placenta and fetal liver. These data revealed region-specific microglial morphology alterations in fetal brain and in inflammatory gene expression in the placenta and fetal liver (specifically, Tnf, Tlr2, Tlr4, and Itgam) due to maternal choline supplementation and/or maternal air pollution exposure. We found that DEP led to changes in microglial morphology in the fetal dentate gyrus of E18 male, but not female, fetuses. In the placenta and fetal liver of males, inflammatory gene expression was affected by both DEP and maternal choline supplementation. However, maternal choline supplementation alone upregulated inflammatory gene expression in females, which may indicate an alteration in maturation rate. These data further contribute to the growing literature indicating region- and tissue-specificity in the developmental immune system in the context of maternal exposures.

neuroscience↗

bioRxiv2022

Limbic progesterone receptors regulate spatial memory

Progesterone and its receptors (PRs) participate in mating and reproduction, but their role in spatial declarative memory, is not understood. Male and female mice express PRs in regions that support spatial memory: the hippocampus and entorhinal cortex. PRs were predominantly expressed in excitatory neurons in Pgr-Cre mice injected with AAV-delivered flexed tdTomato. Furthermore, segesterone, a specific PR agonist, activated neurons in the entorhinal cortex (EC) and the hippocampus. We assessed the PR function in these spatial memory circuit neurons by examining the performance of mice lacking this receptor (PRKO) in novel object recognition, object placement, and Y-maze alternation tasks. In the recognition test, wild-type littermates spent significantly more time exploring the new object than male PRKO mice. The EC-specific deletion of PRs was sufficient to induce a deficit in detecting familiar versus never experienced or new objects. We confirmed deficits in spatial memory of PRKO mice by testing them on the Y-maze forced alternation task. In contrast to spatial tasks, PR removal did not alter the response to fear conditioning. PRs also support spatial memory in female mice. These studies provide novel insights into the role of PR in facilitating spatial, declarative memory in males and females, which may help with finding reproductive partners. SIGNIFICANCE STATEMENTBrain progesterone receptors play an essential role in facilitating mating and reproductive behaviors, but their role in spatial memory and, therefore, mate-finding is not described. Principal, excitatory neurons of the entorhinal cortex and hippocampus express progesterone receptors. These receptors facilitate spatial memory in male and female mice, which may enhance mate-finding reproductive function and food foraging.

neuroscience↗

bioRxiv2022

Ablative radiotherapy improves survival in autochthonous cancer mouse models

Genetically engineered mouse models (GEMMs) of cancer are powerful tools to study mechanisms of disease progression and therapy response, yet little is known about how these models respond to multimodality therapy used for curative intent in patients. Radiation therapy (RT) is frequently used to treat localized cancers with curative intent, delay progression of oligometastases, and palliate symptoms of metastatic disease. RT can be combined with surgery, systemic therapy, and/or immunotherapy for definitive treatment of solid tumors. Here we report the development, testing, and validation of a murine platform that faithfully emulates human stereotactic ablative radiotherapy (SABR). We demonstrate that SABR regimens used in clinical practice can be effectively delivered in mouse models and establish the intestinal tract as the dose limiting organ for abdominopelvic radiation with notable, but transient, lymphodepletion. SABR alters tumor stroma and immune environment, improves survival in GEMMs of primary prostate and colorectal cancer, and synergizes with androgen deprivation in prostate cancer. While SABR is capable of fully ablating xenografts it is unable to completely eradicate disease in GEMMs. These data show that some GEMMs are resistant to curative therapy suggesting the existence of treatment-resistant persister cells in these models.

cancer biology↗

bioRxiv2022

Absolute Winding Number Differentiates Spatial Navigation Strategies with Genetic Risk for Alzheimer's Disease

Spatial navigation and orientation are emerging as promising markers for altered cognition in prodromal Alzheimers disease, and even in cognitively normal individuals at risk for Alzheimers disease. The different APOE gene alleles confer various degrees of risk. The APOE2 allele is considered protective, APOE3 is seen as control, while APOE4 carriage is the major known genetic risk for Alzheimers disease. We have used mouse models carrying the three humanized APOE alleles and tested them in a spatial memory task in the Morris water maze. We introduce a new metric, the absolute winding number, to characterize the spatial search strategy, through the shape of the swim path. We show that this metric is robust to noise, and works for small group samples. Moreover, the absolute winding number better differentiated APOE3 carriers, through their straighter swim paths relative to both APOE2 and APOE4 genotypes. Finally, this novel metric was sensitive to sex differences, supporting increased vulnerability in females. We hypothesized differences in spatial memory and navigation strategies are linked to differences in brain networks, and showed that different genotypes have different reliance on the hippocampal and caudate putamen circuits, pointing to a role for white matter connections. Moreover, differences were most pronounced in females. This departure from a hippocampal centric to a brain network approach may open avenues for identifying regions linked to increased risk for Alzheimers disease, before overt disease manifestation. Further exploration of novel biomarkers based on spatial navigation strategies may enlarge the windows of opportunity for interventions. The proposed framework will be significant in dissecting vulnerable circuits associated with cognitive changes in prodromal Alzheimers disease.

neuroscience↗

bioRxiv2021

Flagellum and toxin phase variation impacts intestinal colonization and disease development in a mouse model of Clostridioides difficile infection

Clostridioides difficile is a major nosocomial pathogen that can cause severe, toxin-mediated diarrhea and pseudomembranous colitis. Recent work has shown that C. difficile exhibits heterogeneity in swimming motility and toxin production in vitro through phase variation by site-specific DNA recombination. The recombinase RecV reversibly inverts the flagellar switch sequence upstream of the flgB operon, leading to the ON/OFF expression of flagellum and toxin genes. How this phenomenon impacts C. difficile virulence in vivo remains unknown. We identified mutations in the right inverted repeat that reduced or prevented flagellar switch inversion by RecV. We introduced these mutations into C. difficile R20291 to create strains with the flagellar switch "locked" in either the ON or OFF orientation. These mutants exhibited a loss of flagellum and toxin phase variation during growth in vitro, yielding precisely modified mutants suitable for assessing virulence in vivo. In a hamster model of acute C. difficile infection, the phase-locked ON mutant caused greater toxin accumulation than the phase locked OFF mutant but did not differ significantly in the ability to cause acute disease symptoms. In contrast, in a mouse model, preventing flagellum and toxin phase variation affected the ability of C. difficile to colonize the intestinal tract and to elicit weight loss, which is attributable to differences in toxin production during infection. These results show that the ability of C. difficile to phase vary flagella and toxins influences colonization and disease development and suggest that the phenotypic variants generated by flagellar switch inversion have distinct capacities for causing disease.

microbiology↗

bioRxiv2021

The Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED): Development and validation for use in pediatric populations

It is increasingly understood that moment-to-moment brain signal variability - traditionally modeled out of analyses as mere "noise" - serves a valuable function role and captures properties of brain function related to development, cognitive processing, and psychopathology. Multiscale entropy (MSE) - a measure of signal irregularity across temporal scales - is an increasingly popular analytic technique in human neuroscience. MSE provides insight into the time-structure and (non)linearity of fluctuations in neural activity and network dynamics, capturing the brains moment-to-moment complexity as it operates on multiple time scales. MSE is emerging as a powerful predictor of developmental processes and outcomes. However, differences in data preprocessing and MSE computation make it challenging to compare results across studies. Here, we (1) provide an introduction to MSE for developmental researchers, (2) demonstrate the effect of preprocessing procedures on scale-wise entropy estimates, and (3) establish a standardized EEG preprocessing and entropy estimation pipeline that generates scale-wise entropy estimates that are reliable and capable of differentiating developmental stages and cognitive states. This novel pipeline - the Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED) is fully automated, customizable, and freely available for download from https://github.com/mhpuglia/APPLESEED. The dataset used herein to develop and validate the pipeline is available for download from https://openneuro.org/datasets/ds003710.

neuroscience↗

bioRxiv2021

c-di-GMP inhibits early sporulation in Clostridioides difficile

The formation of dormant spores is essential for the anaerobic pathogen Clostridioides difficile to survive outside of the host gastrointestinal tract. The regulatory pathways and environmental signals that initiate C. difficile spore formation within the host are not well understood. One bacterial second messenger signaling molecule, cyclic diguanylate (c-di-GMP), modulates several physiological processes important for C. difficile pathogenesis and colonization, but the impact of c-di-GMP on sporulation is unknown. In this study, we investigated the contribution of c-di-GMP to C. difficile sporulation. Overexpression of a gene encoding a diguanylate cyclase, dccA, decreased sporulation frequency and early sporulation gene transcription in both the epidemic R20291 and historical 630{Delta}erm strains. Expression of a dccA allele encoding a catalytically inactive DccA that is unable to synthesize c-di-GMP no longer inhibited sporulation, indicating that the accumulation of intracellular c-di-GMP reduces C. difficile sporulation. A null mutation in dccA slightly increased sporulation in R20291 and slightly decreased sporulation in 630{Delta}erm, suggesting that DccA may contribute to the intracellular pool of c-di-GMP in a strain-dependent manner. However, these data were highly variable, underscoring the complex regulation involved in modulating intracellular c-di-GMP concentrations. Finally, overexpression of dccA in known sporulation mutants revealed that c-di-GMP is likely signaling through an unidentified regulatory pathway to control early sporulation events in C. difficile. C-di-GMP-dependent regulation of C. difficile sporulation may represent an unexplored avenue of potential environmental and intracellular signaling that contributes to the complex regulation of sporulation initiation. IMPORTANCEMany bacterial organisms utilize the small signaling molecule cyclic diguanylate (c-di-GMP) to regulate important physiological processes, including motility, toxin production, biofilm formation, and colonization. C-di-GMP inhibits motility and toxin production and promotes biofilm formation and colonization in the anaerobic, gastrointestinal pathogen Clostridioides difficile. However, the impact of c-di-GMP on C. difficile spore formation, a critical step in this pathogens life cycle, is unknown. Here, we demonstrate that c-di-GMP negatively impacts sporulation in two clinically relevant C. difficile strains, the epidemic R20291 and the historical 630{Delta}erm. The pathway through which c-di-GMP controls sporulation was investigated, and our results suggest that c-di-GMP is likely signaling through an unidentified regulatory pathway to control C. difficile sporulation. This work implicates c-di-GMP metabolism as a potential mechanism to integrate environmental and intracellular cues through c-di-GMP levels to influence C. difficile sporulation.

microbiology↗

bioRxiv2019

The DNA end-binding protein Ku associates with human telomeres primarily via protein-protein interactions

The Ku heterodimer (Ku70/Ku80) binds DNA ends with high affinity but without sequence specificity and, upon binding ends created by double-stranded breaks (DSBs), initiates canonical nonhomologous end-joining (c-NHEJ). Ku also localizes to functional telomeres where its c-NHEJ activity is inhibited. Interestingly, Ku has been co-opted at telomeres across species, where it performs varied telomeric functions. In humans, Ku is essential for its role in telomere maintenance, but how it associates with human telomeres is not known. Analysis of Kus telomere association in different populations of cen3tel cells, which had a wide range of average telomere lengths, supported Kus localization at human telomeres primarily via protein-protein interaction. We also found that the Ku70 and Ku80 5 helices, which are on opposing sides of the heterodimer and were previously implicated in Saccharomyces cerevisiae Kus NHEJ and telomeric functions, respectively, participated in Kus telomere association in human cells. While the Ku70 5 mutant showed increased interaction with TRF2, the Ku80 5 mutant was not impacted for TRF2 association. Interestingly, residues altered to impair Kus DNA end-binding function were also involved in TRF2 interaction and telomere association. Overall, our results suggest protein-protein interactions as the primary mode by which Ku associates with human telomeres.

molecular biology↗

bioRxiv2018

Gut microbiota and phytoestrogen-associated infertility in southern white rhinoceros

With recent poaching of southern white rhinoceros (Ceratotherium simum simum; SWR) reaching record levels, the need for a robust assurance population is urgent. However, the global captive SWR population is not currently self-sustaining due to the reproductive failure of captive-born females. Dietary phytoestrogens have been proposed to play a role in this phenomenon, and recent work has demonstrated a negative relationship between diet estrogenicity and fertility of captive-born female SWR. To further examine this relationship, we compared gut microbial communities, fecal phytoestrogens, and fertility of SWR to another rhinoceros species-the greater one-horned rhinoceros (Rhinoceros unicornis; GOHR), which consumes a similar diet but exhibits high levels of fertility in captivity. Using 16S rRNA amplicon sequencing and mass spectrometry, we identified a species-specific fecal microbiota and three dominant fecal phytoestrogen profiles. These profiles exhibited varying levels of estrogenicity when tested in an in vitro estrogen receptor activation assay for both rhinoceros species, with profiles dominated by the microbial metabolite, equol, stimulating the highest levels of receptor activation. Finally, we found that SWR fertility varies significantly with respect to phytoestrogen profile, but also with the abundance of several bacterial taxa and microbially-derived phytoestrogen metabolites. Taken together, these data suggest that in addition to species differences in estrogen receptor sensitivity to phytoestrogens, reproductive outcomes may be driven by gut microbiotas transformation of dietary phytoestrogens in captive SWR females.

microbiology↗