Biology subjects

Gill, J.

Publications and source records attributed to Gill, J..

17 recordsLinked to original sources

bioRxiv2025

Circulating Lipids are Associated with PTSD Severity and Predict Symptomatic PTSD in a Cohort of Veterans and Service Members

Post-traumatic stress disorder (PTSD) is characterized by chronic stress, alterations in mood, and avoidance after a traumatic event has occurred. While recovery can occur, many PTSD patients suffer life-long impairments. In combat veterans, high rates of PTSD contribute to increased rates of depression and anxiety and a higher likelihood of suicidal ideation. The lack of biological markers for psychiatric conditions such as PTSD highlights the need for omics-based approaches to diagnosis. Discovery of novel blood-based biomarkers could aid in the development of treatments or therapies, quantify groups for those at the highest risk of adverse events, and provide insight into the molecular underpinnings of PTSD. This study used untargeted lipidomics to analyze 602 circulating lipid species in blood from a cohort of 133 veterans and combat members with varying severities of PTSD. We discovered five circulating lipids, including serum total cholesterol, cholesterol ether (ChE(18:2)), and lipids associated with metabolic dysfunction (cardiolipin : CL(87:7), monolysocardiolipin : MLCL(50:4), and phosphatidylethanolamine plasmalogen/ether lipid : PE(18:1e_20:3)) that correlated significantly with increasing PTSD severity after adjustment for multiple comparisons. Additionally, we showed that symptomatic PTSD patients could be separated from asymptomatic controls using these lipid species. This study contributes to the limited research surrounding the role of circulating lipids in PTSD.

neuroscience↗

bioRxiv2025

Impact of > 24 h sustained wakefulness and subsequent recovery sleep on time-dependent changes in microRNA factors of individuals with post-acute phase mild traumatic brain injury

IntroductionThe purpose of the present study was to determine whether mild traumatic brain injury (mTBI+) results in latent changes in microRNA expression profiles across an episode of total sleep deprivation (TSD). MethodsSeven previously concussed (mTBI+) adults (24.5 {+/-} 5.3 y.o.) and 6 non-concussed control adults (mTBI-; 24.8 {+/-} 1.6 y.o.) underwent 24 h TSD (T2) preceded by 8 h baseline sleep (T1; BSL) and followed by 8 h recovery (T3; REC) sleep. Salivary microRNA expression was assessed across the entire study. ResultsSubjects (mTBI+ and mTBI-) had differential expression of salivary microRNA targets across TSD. mTBI+ subjects had greater change to microRNA expression profiles compared to mTBI- subjects between T1 and T3. DiscussionAlthough there is some evidence that TSD may unmask latent changes in gene expression in mTBI+ subjects, a definitive conclusion was precluded by differences in baseline sleep in mTBI+ (vs. mTBI-) subjects measured through polysomnography (not shown). However, this study is unique in that the mTBI+ subjects were exposed to a sleep deprivation challenge very shortly after medical clearance from mTBI demonstrating lingering neurobiological impacts of mTBI.

neuroscience↗

bioRxiv2025

PRISM: A platform for illuminating viral dark matter

The exploration of bacteriophage diversity remains constrained by reliance on conventional plaque assays, which bias discovery toward phages that form visible plaques and propagate efficiently. The discovery process, as well as measuring correct phage concentrations and phage resistance frequencies, are also time-consuming and labor intensive. Here, we present PRISM (Phage Recovery and Investigation in Single-droplet Microenvironments), a droplet microfluidics-based, plating-independent platform for the high-throughput isolation, quantification, and characterization of bacteriophages. By encapsulating phage-host interactions in water-in-oil microdroplets at single-phase resolution, and then coupling them with fluorescence-based detection and sorting at million-droplet scale, PRISM enables rapid identification of novel phages, including those that evade detection in conventional assays. We demonstrate PRISMs capabilities across several key applications: (i) recovery of both novel "plaquing" and "non-plaquing" Salmonella phages from a concentrated environmental sample, where PRISM recovered multiple representatives of a non-plaquing genus completely missed by conventional plating-based approaches; (ii) accurate titering of poor-plaquing phages such as Rhodococcus phage ReqiDocB7, for which PRISM reported a 2-fold higher titer than conventional plaque assays; and (iii) plating-free determination of phage resistance frequency, with PRISM yielding resistance and lysogeny frequencies (e.g., 1 in 4.4 x 105 cells for T7 Escherichia phage resistance and 1 in 21 cells for Escherichia Lambda phage lysogeny) that closely match conventional estimates. These data highlight PRISMs enhanced resolution and accuracy, as well as its ability to detect rare, non-plaquing, or slow-replicating phages, in a high speed and automated fashion, thereby underscoring the platforms power to access viral "dark matter" traditionally overlooked using conventional methods.

microbiology↗

bioRxiv2025

Elevations in plasma proinsulin predict the development of diabetes in NOD mice

The global incidence of type 1 diabetes (T1D) continues to rise, yet reliable biomarkers for predicting disease onset remain limited. Studies have demonstrated persistent proinsulin secretion in individuals living with T1D, suggesting a processing impairment. Proinsulin is processed into mature active insulin by the prohormone convertases PC1/3, PC2, and carboxypeptidase E. We hypothesized that elevated circulating proinsulin-to-C-peptide (PI:C) ratios precede the onset of diabetes and are associated with reduced expression of PC1/3 in pancreatic beta cells. Non-obese diabetic (NOD) mice were monitored for changes in plasma proinsulin, C-peptide, and beta cell Pc1/3 levels prior to diabetes onset. Female NOD mice that progressed to diabetes exhibited increased plasma proinsulin and PI:C ratios several weeks before the onset of diabetes compared to mice that remained normoglycemic. Plasma proinsulin levels were predictive of diabetes onset, with earlier elevations observed in mice that progressed to disease more rapidly. These increases in plasma proinsulin and PI:C ratios correlated with reduced beta cell Pc1/3 expression. These findings support the potential of plasma proinsulin and PI:C ratios as predictive biomarkers for T1D development and implicate diminished Pc1/3 expression as a possible mechanism underlying impaired proinsulin processing.

cell biology↗

bioRxiv2025

Neonatal mimicry of caregivers at home: feasibility of an asynchronous online paradigm

While early life sets the stage for later learning, comparatively less is known about newborns cognition than that of older infants. A striking example is the lack of consensus regarding the extent to which newborns spontaneously mimic gestures, and whether such behavior drives bonding and learning. Despite the theoretical importance of these questions, practical challenges limit researchers ability to engage newborns in behavioral research. Webcam-based, asynchronous online studies have expanded developmental sciences capacity to reach older infants. However, such scalable and replicable methods have yet to be deployed with younger infants. Taking a commonly-used neonatal mimicry paradigm as a test case, we assessed the feasibility of leveraging an open-source online platform (Children Helping Science) for asynchronous research with 0-6-week-olds and their caregivers. Caregivers modeled face movements to their 4-45 days-old infants (N = 29, N = 17 included) while webcams filmed their infants responses; 13 dyads participated more than once (72 included test videos). There was preliminary, moderate evidence against group-level neonatal mimicry of caregivers tongue protrusions (Bayes Factor [~] [1/3]), and inconclusive evidence for or against mimicry of caregivers mouth openings ([1/3] < BF < 3). Simulations identified a target sample size for more conclusive evidence. Finally, we asked whether caregivers perceived their newborns behavior as imitative. Caregivers perceptions of mimicry reflected infants behaviors but did not align with an often-used metric of mimicry ("imitators"). These results demonstrate the feasibility of asynchronous online behavioral studies with newborns and provide a foundation for future research on neonatal mimicry of caregivers.x1

neuroscience↗

bioRxiv2025

Early pandemic HIV-1 integration site preferences differ across anatomical reservoirs

Despite effective viral suppression with modern antiretroviral therapy (ART), HIV-1 persists in latent reservoirs across multiple tissues. Integration into the host genome is essential for viral persistence, yet the characteristics of these reservoir sites across anatomical locations remain poorly understood. To address this, we analyzed integration sites from matched esophagus, PBL/PBMC, stomach, duodenum, colon, and unmatched brain tissue samples of individuals infected with HIV-1 subtype B. The virus used in this study was from 1993, an early stage of the HIV pandemic, providing insights into integration patterns before extensive ART use. Our analysis examined genomic feature enrichment, proximity to non-B DNA structures, integration hotspots, and site overlap across tissues and individuals. We identified a distinct integration pattern in brain tissue, characterized by reduced gene targeting and increased enrichment in Short Interspersed Nuclear Elements (SINEs) and DNase I hypersensitivity sites (DHS). Tissue-specific preferences for integration near non-B DNA structures were evident, alongside shared and unique hotspots across tissues and individuals. Notably, genes associated with HIV-related diseases were frequent integration targets. These findings underscore the complex interplay between viral integration, host genetics, and tissue-specific factors, highlighting the potential role of integration sites in disease development.

microbiology↗

bioRxiv2024

Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell

Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools. To fill this need we developed Apollo, a GPU-accelerated, out-of-core tool for within-host simulation of viral evolution and infection dynamics across population, tissue, and cellular levels. Apollo is scalable to hundreds of millions of viral genomes and can handle complex demographic and population genetic models. Apollo can replicate real within-host viral evolution; accurately recapturing observed viral sequences from an HIV cohort derived from initial population-genetic configurations. For practical applications, using Apollo-simulated viral genomes and transmission networks, we validated and uncovered the limitations of a widely used viral transmission inference tool.

bioinformatics↗

bioRxiv2024

The Mitochondrial Ubiquitin Ligase MARCHF5 Cooperates with MCL1 to Inhibit Apoptosis in KSHV-Transformed Primary Effusion Lymphoma Cell Lines

Kaposis sarcoma-associated herpesvirus (KSHV) causes several malignancies in people with HIV including Kaposis sarcoma and primary effusion lymphoma (PEL). We have previously shown that PEL cell lines require myeloid cell leukemia-1 (MCL1) to inhibit apoptosis. MCL1 is an oncogene that is amplified in cancers and causes resistance to chemotherapy regimens. MCL1 is thus an attractive target for drug development. The emerging clinical relevance and therapeutic potential of MCL1 motivated us to study the roles of this oncogene in PEL in depth. Using a systems biology approach, we uncovered an unexpected genetic interaction between MCL1 and MARCHF5 indicating that they function in the same pathway. MARCHF5 is an E3 ubiquitin ligase most known for regulating mitochondrial homeostasis and antiviral signaling, but not apoptosis. We thus investigated how MCL1 and MARCHF5 cooperate to promote PEL cell survival. CRISPR knockout (KO) of MARCHF5 in PEL cell lines resulted in a significant increase in apoptosis despite the presence of MCL1. The anti-apoptotic function of MARCHF5 was dependent on its E3 ligase and dimerization activities. Loss of MARCHF5 or inhibition of the 26S proteasome furthermore stabilized the MCL1 antagonist NOXA without affecting levels of MCL1. Interestingly, NOXA KO provides a fitness advantage to PEL cells suggesting that NOXA is the pro-apoptotic signal that necessitates the anti-apoptotic activities of MCL1 and MARCHF5. Finally, endogenous reciprocal co-immunoprecipitation experiments show that MARCHF5 and NOXA are found in the same protein complex. Our findings thus provide the mechanistic link that underlies the genetic interaction between MCL1 and MARCHF5. We propose that MARCHF5 induces the degradation of the MCL1 antagonist NOXA thus reinforcing the pro-survival role of MCL1 in these tumor cells. This newly appreciated interaction of the MCL1 and MARCHF5 oncogenes may be useful to improve the design of combination therapies for KSHV malignancies.

cancer biology↗

bioRxiv2024

Targeting DBS to the centrolateral thalamic nucleus improves movement in a lesion-based model of acquired cerebellar dystonia in mice

Dystonia is the third most common movement disorder and an incapacitating co-morbidity in a variety of neurologic conditions. Dystonia can be caused by genetic, degenerative, idiopathic, and acquired etiologies, which are hypothesized to converge on a "dystonia network" consisting of the basal ganglia, thalamus, cerebellum, and cerebral cortex. In acquired dystonia, focal lesions to subcortical areas in the network - the basal ganglia, thalamus, and cerebellum - lead to a dystonia that can be difficult to manage with canonical treatments, including deep brain stimulation (DBS). While studies in animal models have begun to parse the contribution of individual nodes in the dystonia network, how acquired injury to the cerebellar outflow tracts instigates dystonia; and how network modulation interacts with symptom latency remain as unexplored questions. Here, we present an electrolytic lesioning paradigm that bilaterally targets the cerebellar outflow tracts. We found that lesioning these tracts, at the junction of the superior cerebellar peduncles and the medial and intermediate cerebellar nuclei, resulted in acute, severe dystonia. We observed that dystonia is reduced with one hour of DBS of the centrolateral thalamic nucleus, a first order node in the network downstream of the cerebellar nuclei. In contrast, one hour of stimulation at a second order node in the short latency, disynaptic projection from the cerebellar nuclei, the striatum, did not modulate the dystonia in the short-term. Our study introduces a robust paradigm for inducing acute, severe dystonia, and demonstrates that targeted modulation based on network principles powerfully rescues motor behavior. These data inspire the identification of therapeutic targets for difficult to manage acquired dystonia.

neuroscience↗

bioRxiv2024

Multiregional Representations of Intertemporal Decision Making in Human Single Neurons

Characterization of the neural basis of delay discounting provides insight into the origin of impulsive decision-making, which underlies several psychiatric diseases including substance use disorder. Here, we identify human single unit representations of decisions, and their level of difficulty, in the orbitofrontal cortex, hippocampus and amygdala that are related to preferences for immediate vs. delayed rewards. Results provide an initial account of multiregional intracranial computations related to impulsive behaviors in humans.

neuroscience↗

bioRxiv2023

Interactions between the gut microbiome, dietary restriction, and aging in genetically diverse mice

The intestinal microbiome changes with age, but the causes and consequences of microbiome aging remain unclear. Furthermore, the gut microbiome has been proposed to mediate the benefit of lifespan- extending interventions such as dietary restriction, but this hypothesis warrants further exploration. Here, by analyzing 2997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice, we provide new insights into the interplay between the microbiome, aging, dietary restriction, host genetics, and a wide range of health parameters. First, we find that microbiome uniqueness increases with age across datasets and species. Moreover, age-associated changes are better explained by cumulative exposure to stochastic events (neutral theory) than by the influence of an aging host (selection theory). Second, we unexpectedly find that the majority of microbiome features are significantly heritable and that the amount of variation explained by host genetics is as large as that of aging and dietary restriction. Third, we find that the intensity of dietary restriction parallels the extent of microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is significantly associated with multiple health parameters -- including body composition, immune parameters, and frailty -- but not with lifespan. In summary, this large and multifaceted study sheds light on the factors influencing the microbiome and aspects of host physiology modulated by the microbiome.

microbiology↗

bioRxiv2023

Neuronal Tau Pathology Worsens Late Phase White Matter Degeneration After Traumatic Brain Injury in Transgenic Mice

Traumatic brain injury (TBI) causes diffuse axonal injury which can produce chronic white matter pathology and subsequent post-traumatic neurodegeneration with poor patient outcomes. Tau modulates axon cytoskeletal functions and undergoes phosphorylation and mis-localization in neurodegenerative disorders. The effects of tau pathology on neurodegeneration after TBI are unclear. We used mice with neuronal expression of human mutant tau to examine effects of pathological tau on white matter pathology after TBI. Adult male and female hTau.P301S (Tg2541) transgenic and wild type (Wt) mice received either moderate single TBI (s-TBI) or repetitive mild TBI (r-mTBI; once daily x 5), or matched sham procedures. Acutely, s-TBI produced more extensive axon damage in the corpus callosum (CC) as compared to r-mTBI. After s-TBI, significant CC thinning was present at 6 weeks and 4 months post-injury in Wt and transgenic mice, with homozygous tau expression producing additional pathology of late demyelination. In contrast, r-mTBI did not produce significant CC thinning except at the chronic time point of 4 months in homozygous mice, which exhibited significant CC atrophy (-29.7%) with increased CC microgliosis, but not astrogliosis. Serum biomarker quantification demonstrated neurofilament light detection of early axonal damage one day post-injury in Wt and homozygous mice. At 4 months, high tau and neurofilament in homozygous mice implicated tau in chronic axon pathology. Conclusions: Neuronal tau pathology differentially exacerbated CC pathology based on injury severity and chronicity. Ongoing CC atrophy from s-TBI became accompanied by late demyelination. Pathological tau significantly worsened CC atrophy during the chronic phase after r-mTBI.

neuroscience↗

bioRxiv2022

Cooperativity between Cas9 and AID establishes broad and diversifying mutational footprints in base editors

The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding of how Cas9 and DNA deaminases collaborate to shape base editor (BE) outcomes has been lacking. Here, we support a novel mechanistic model of base editing by deriving a range of hyperactive activation-induced deaminase (AID) base editors (hBEs) and exploiting their characteristic diversifying activity. Our model involves multiple layers of previously underappreciated cooperativity in BE steps including: (1) Cas9 binding can potentially expose both DNA strands for capture by the deaminase, a feature that is enhanced by guide RNA mismatches; (2) after strand capture, the intrinsic activity of the DNA deaminase can tune window size and base editing efficiency; (3) Cas9 defines the boundaries of editing on each strand, with deamination blocked by Cas9 binding to either the PAM or the protospacer; and (4) non-canonical edits on the guide RNA bound strand can be further elicited by changing which strand is nicked by Cas9. Leveraging insights from our mechanistic model, we create novel hBEs that can remarkably generate simultaneous C>T and G>A transitions over >65 bp with significant potential for targeted gene diversification.

biochemistry↗

bioRxiv2022

Expression Ratios of the Anti-Apoptotic BCL2 Family Members Dictate the Selective Addiction of KSHV-Transformed Primary Effusion Lymphoma Cell Lines to MCL1

Kaposis sarcoma-associated herpesvirus (KSHV) causes several malignancies in people living with HIV, including primary effusion lymphoma (PEL). PEL cell lines exhibit oncogene addictions to both viral and cellular genes. Using CRISPR screens, we previously identified cellular oncogene addictions in PEL cell lines, including MCL1. MCL1 is a member of the BCL2 family, which functions to prevent intrinsic apoptosis and has been implicated in several cancers. Despite the overlapping functions of the BCL2 family members, PEL cells are only dependent on MCL1 suggesting that MCL1 may have non-redundant functions. To investigate why PEL cells exhibit selective addiction to MCL1, we inactivated the intrinsic apoptosis pathway by engineering BAX/BAK1 double knockout cells. In this context, PEL cells become resistant to MCL1 knockdown or MCL1 inactivation by the MCL1 inhibitor S63845, indicating that the main function of MCL1 in PEL cells is to prevent BAX/BAK1-mediated apoptosis. The selective requirement to MCL1 is due to MCL1 being expressed in excess over the BCL2 family. Ectopic expression of several BCL2 family proteins, as well as the KSHV BCL2 homolog, significantly decreased basal caspase 3/7 activity and buffered against staurosporine-induced apoptosis. Finally, over-expressed BCL2 family members can functionally substitute for MCL1, when it is inhibited by S63845. Together our data indicate that the expression levels of the BCL2 family likely explain why PEL tumor cells are highly addicted to MCL1. Importantly, our results suggest that caution should be taken when considering MCL1i as a monotherapy regimen for PEL, because resistance can easily develop. IMPORTANCEPrimary effusion lymphoma (PEL) is caused by Kaposis sarcoma-associated herpesvirus. We previously showed that PEL cell lines require the anti-apoptotic protein MCL1 for survival, but not the other BCL2 family proteins. This selective dependence to MCL1 is unexpected as the BCL2 family functions similarly in preventing intrinsic apoptosis. Recently, new roles for MCL1 not shared with the BCL2 family have emerged. Here, we show that non-canonical functions of MCL1 are unlikely essential. Instead, MCL1 mainly functions to prevent apoptosis. The specific requirement to MCL1 is due to MCL1 being expressed in excess over the BCL2 family. Consistent with this model, shifting these expression ratios changes the requirement away from MCL1 and towards the dominant BCL2 family gene. Together, our results indicate that although MCL1 is an attractive chemotherapeutic target to treat PEL, careful consideration must be taken as resistance to MCL1-specific inhibitors easily develops through BCL2 family overexpression.

microbiology↗

bioRxiv2022

3' RNA sequencing does not increase power or reduce costs for gene expression analysis

BackgroundSequencing RNA transcripts for gene expression profiling is a popular and important technique with broad utility in biological sciences. We set out to comprehensively compare the two most popular methods for generating sequencing libraries for differential gene expression analysis: 3-end sequencing, which generates libraries from the 3 end of an RNA transcript; and traditional RNA sequencing, which generates libraries from whole RNA transcripts. We include three species in our experiment to test whether our findings replicate across genomes and genome assemblies. ResultsWe found similar levels of precision and power to detect differentially expressed genes between the two methods. Notably, whole transcript RNA-seq performed better in the non-traditional model species included in our study. ConclusionOverall, we recommended whole transcript RNA sequencing for the added benefits of alternative splicing detection, and gene-body variant detection.

genomics↗

bioRxiv2018

PCSK9 genetic variants, life-long lowering of LDL-cholesterol and cognition: a large-scale Mendelian randomization study

AimsPCSK9 inhibitors lower LDL cholesterol and are efficacious at reducing risk of vascular disease, however questions remain about potential adverse effects on cognitive function. We examined the association of LDL cholesterol-lowering genetic variants in PCSK9 with continuous measures of cognitive ability\n\nMethods and ResultsSix independent SNPs in PCSK9 were used in up to 337,348 individuals from the UK Biobank who underwent measures of cognitive ability (fluid reasoning, reaction time, trial making test and digit symbol coding. Scaled to a 50mg/dL lower LDL cholesterol, the PCSK9 allele score was associated with a lower risk of CHD (odds ratio 0.73; 95% CI: 0.60 to 0.90, P = 0.003). The scaled PCSK9 allele score nominally associated with worse log reaction time (0.04 standard deviations; 95%CI: 0.00, 0.08; P=0.038). Although no strong associations of the PCSK9 allele score were identified with any cognitive trait, the imprecision around the estimates meant that we could not exclude a similar magnitude of effect of genetic inhibition of PCSK9 to that seen with established risk factors, including APOEe4 or smoking status for any of the individual cognition traits. Point estimates for the PCSK9 allele score and cognition traits were all on the harmful side of unity.\n\nConclusionsUsing currently available data in UK Biobank, we are not able to rule out meaningful associations of PCSK9 genetic variants with cognition traits. These data highlight the need for further large-scale genetic analyses and, in parallel, continued pharmacovigilance for patients currently treated with PCSK9 inhibitors.

epidemiology↗

bioRxiv2018

Antimicrobial peptides modulate long-term memory

Antimicrobial peptides act as a host defense mechanism and regulate the commensal microbiome. To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from single Drosophila heads following behavioral training that produces long-lasting memory. Surprisingly, we find that two immune peptides with antimicrobial activity, Diptericin B and Gram-Negative Bacteria Binding Protein like 3, regulate long-term but not short-term memory or instinctive behavior in Drosophila. The cellular requirement of these two peptides is distinct: head fat body for DptB, and neurons for GNBP-like3. That antimicrobial peptides influence memory provides a novel example of the emerging link between the immune and nervous systems and reveals that some immune peptides may have been repurposed in the nervous system.

neuroscience↗