Biology subjects

Miller, J.

Publications and source records attributed to Miller, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Vascular tortuosity quantification as an outcome metric of the oxygen-induced retinopathy model of ischemic retinopathy

The murine oxygen-induced retinopathy (OIR) model is one of the most widely used animal models of ischemic retinopathy, mimicking hallmark pathophysiology of initial vaso-obliteration (VO) resulting in ischemia that drives neovascularization (NV). In addition to NV and VO, human ischemic retinopathies including Retinopathy of Prematurity (ROP) are characterized by increased vascular tortuosity. Vascular tortuosity is an indicator of disease severity, need to treat, and treatment response in ROP. Current literature investigating novel therapeutics in the OIR model report their effects on NV and VO, but no standardized quantification of vascular tortuosity exists to date despite this metrics relevance to human disease in clinics. The current proof-of-concept study applied a computer-based image analysis algorithm capable of calculating standardized measurements of vascular tortuosity. Quantification of vascular tortuosity correlated with disease activity in OIR analogously to that observed in infants with ROP. Treatment of OIR mice with anti-Vascular Endothelial Growth Factor (aflibercept) rescued vascular tortuosity in the model. Altogether, these data demonstrated that vascular tortuosity is a quantifiable feature of the OIR model and may be used as an outcome measurement in future studies investigating new treatment modalities for retinal ischemia.

neuroscience↗

bioRxiv2022

Optimal feature selection and software tool development for bacteriocin prediction

Antibiotic resistance is a major public health concern around the globe. As a result, researchers always look for new compounds to develop new antibiotic drugs for combating antibiotic-resistant bacteria. Bacteriocin becomes a promising antimicrobial agent to fight against antibiotic resistance, due to its narrow killing spectrum. Sequence matching methods are widely used to identify bacteriocins by comparing them with the known bacteriocin sequences; however, these methods often fail to detect new bacteriocin sequences due to sequences high diversity. The ability to use a machine learning approach can help find new highly dissimilar bacteriocins for developing highly effective antibiotic drugs. The aim of this work is to identify optimal sets of features and develop a machine learning-based software tool for predicting bacteriocin protein sequences with high accuracy. We extracted potential features from known bacteriocin and non-bacteriocin sequences by considering the physicochemical and structural properties of the protein sequences. Then we reduced the feature set using statistical justifications and recursive feature elimination technique. Finally, we built support vector machine (SVM) and random forest (RF) models using the selected features and our models can achieve accuracy up to 95.54%. We compared the performance of our method with a popular sequence matching-based approach and a deep learning-based method. We also developed a software tool called Bacteriocin Prediction (BacPred) that implements the prediction model using the optimal set of features obtained from this study. The software package and its user manual are available at https://github.com/suraiya14/ML_bacteriocins/BacPred.

bioinformatics↗

bioRxiv2022

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

The orb-web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for Araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the two X chromosomes for U. diversus and identify candidate sex-determining genes. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex-determination in spiders.

genomics↗

bioRxiv2022

Long-term learning transforms prefrontal cortex selectivity during working memory

The lateral prefrontal cortex (lPFC) is reliably active during working memory (WM) across human and animal models, but the role of lPFC in successful WM is under debate. For instance, non-human primate (NHP) electrophysiology research finds that lPFC circuitry stores WM representations. Human neuroimaging instead suggests that lPFC plays a control function over WM content that is stored in sensory cortices. These seemingly incompatible WM accounts are often confounded by differences in the amount of task training and stimulus exposure across studies (i.e., NHPs tend to be trained extensively). Here, we test the possibility that such long-term training may alter the role of lPFC in WM maintenance. We densely sampled WM-related activity across learning, in three human participants, using a longitudinal functional MRI (fMRI) protocol. Over three months, participants trained on (1) a serial reaction time (SRT) task, wherein complex fractal stimuli were embedded within probabilistic sequences, and (2) a delayed recognition task probing WM for trained or novel stimuli. Participants were scanned frequently throughout training, to track how WM activity patterns change with repeated stimulus exposure and long-term associative learning. WM task performance improved for trained (but not novel) fractals and, neurally, delay activity significantly increased in distributed lPFC voxels across learning. Pattern similarity analyses also found that item-level WM representations became detectable within lPFC, but not in sensory cortices, and lPFC delay activity increasingly reflected sequence relationships from the SRT task, even though that information was task-irrelevant for WM. These findings demonstrate that human lPFC can show stimulus-selective WM responses with learning and WM representations are shaped by long-term experience. Therefore, influences from training and long-term memory may reconcile competing accounts of lPFC function during WM.

neuroscience↗

bioRxiv2022

Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques

BackgroundThe rapid spread of the SARS-CoV-2 Omicron (B.1.1.529) variant, including in highly vaccinated populations, has raised important questions about the efficacy of current vaccines. Immune correlates of vaccine protection against Omicron are not known. Methods30 cynomolgus macaques were immunized with homologous and heterologous prime-boost regimens with the mRNA-based BNT162b2 vaccine and the adenovirus vector-based Ad26.COV2.S vaccine. Following vaccination, animals were challenged with the SARS-CoV-2 Omicron variant by the intranasal and intratracheal routes. ResultsOmicron neutralizing antibodies were observed following the boost immunization and were higher in animals that received BNT162b2, whereas Omicron CD8+ T cell responses were higher in animals that received Ad26.COV2.S. Following Omicron challenge, sham controls showed more prolonged virus in nasal swabs than in bronchoalveolar lavage. Vaccinated macaques demonstrated rapid control of virus in bronchoalveolar lavage, and most vaccinated animals also controlled virus in nasal swabs, showing that current vaccines provide substantial protection against Omicron in this model. However, vaccinated animals that had moderate levels of Omicron neutralizing antibodies but negligible Omicron CD8+ T cell responses failed to control virus in the upper respiratory tract. Virologic control correlated with both antibody and T cell responses. ConclusionsBNT162b2 and Ad26.COV2.S provided robust protection against high-dose challenge with the SARS-CoV-2 Omicron variant in macaques. Protection against this highly mutated SARS-CoV-2 variant correlated with both humoral and cellular immune responses.

microbiology↗

bioRxiv2021

Mathematical modeling suggests cooperation of plant-infecting viruses

Viruses are major pathogens of agricultural crops. Viral infections often start after the virus enters the outer layer of a tissue or surface and many successful viruses, after local replication in the infected tissue, are able to spread systemically. Quantitative details of virus dynamics in plants, however, have been poorly understood, in part, because of the lack of experimental methods allowing to accurately measure the degree of infection in individual plant tissues. Recently, by using flow cytometry and two different flourescently-labeled strains of the Tobacco etch virus (TEV), Venus and BFP, kinetics of viral infection of individual cells in leaves of Nicotiana tabacum plants was followed over time [1]. A simple mathematical model, assuming that viral spread occurs from lower to upper leaves, was fitted to these data. While the the original model could accurately describe the kinetics of viral spread locally and systemically, we also found that many alternative versions of the model, for example, if viral spread starts at upper leaves and progresses to lower leaves or when virus dissemination is stopped due to an immune response, provided fits of the data with reasonable quality, and yet with different parameter estimates. These results strongly suggest that experimental measurements of the virus infection in individual leaves may not be sufficient to identify the pathways of viral dissemination between different leaves and reasons for viral control; we propose experiments that may allow discrimination between the alternatives. By analyzing the kinetics of coinfection of individual cells by Venus and BFP strains of TEV we found a strong deviation from the random infection model, suggesting cooperation between the two strains when infecting plant cells. Importantly, we showed that many mathematical models on the kinetics of coinfection of cells with two strains could not adequately describe the data, and the best fit model needed to assume i) different susceptibility of uninfected cells to infection by two viruses locally in the leaf vs. systemically from other leaves, and ii) decrease in the infection rate depending on the fraction of uninfected cells which could be due to a systemic immune response. Our results thus demonstrate the difficulty in reaching definite conclusions from extensive and yet limited experimental data and provide evidence of potential cooperation between different viral variants infecting individual cells in plants.

microbiology↗

bioRxiv2021

Conservation and divergence in cortical cellular organization between human and mouse revealed by single-cell transcriptome imaging

The human cerebral cortex has tremendous cellular diversity and complex cellular organization that are essential for brain function. How different types of cells are organized and interact with each other in the human cortex, and how cellular organizations and interaction patterns vary across species are, however, unclear. Here, we performed spatially resolved single-cell expression profiling of 4,000 genes in human middle and superior temporal gyrus using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We identified >100 neuronal and non-neuronal cell populations with distinct transcriptional signatures, generated a molecularly defined and spatially resolved cell atlas of these brain regions, and analyzed cell-cell interactions in a cell-type-specific manner. Comparison with the mouse cortex showed conservation in the laminar organization of cells and substantial divergence in cell-cell interactions between human and mouse. Notably, our data revealed a drastic increase in interactions between neurons and non-neuronal cells in the human cortex, uncovered human-specific cell-cell interaction patterns, and identified potential ligand-receptor basis of microglia-neuron interactions.

neuroscience↗

bioRxiv2021

The crucial role of genome-wide genetic variation in conservation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on the conservation of genome-wide genetic variation, and that this approach should be replaced with another that focuses instead on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that the conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations towards extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide variation on long-term population viability will only worsen the biodiversity crisis.

evolutionary biology↗

bioRxiv2021

Using stationary vital rates in impact assessments may underestimate potential threat

Population viability analysis (PVA) is commonly used to assess future potential risks to threatened species. These models are typically based on mean vital rates, such as survival and fecundity, with some level of environmental stochasticity. However, the vital rates of wild populations, especially those already exhibiting declining trajectories, may be nonstationary, such that the mean or variance changes over time. In this study, we examined whether including observed temporal trends in vital rates affects the predictive accuracy of PVA, as well as the projected impact associated with a hypothetical threat. To achieve this, we ran a series of simulations using Leslie matrix PVA models that included different combinations of environmental stochasticity, temporal trends in vital rates, and threat. We apply our analysis to a long-lived colonial species of seabird, the black-legged kittiwake Rissa tridactyla, that is classified as globally Vulnerable and is potentially highly sensitive to offshore renewable energy development. We found that including observed temporal trends in vital rates was (i) crucial for the accurate reconstruction of observed population dynamics and (ii) had a dramatic effect on the projected impact from the hypothetical threat. In an era when many animal and plant populations are declining due to long-term trends in their vital rates, we identify that including this demographic structure is essential for robustly evaluating potential threats using PVA models. Omitting observed temporal trends in vital rates from impact assessments is highly likely to yield unreliable results that could misinform conservation and management decision making. This result has immediate application for conducting impact assessments on protected species and populations.

ecology↗

bioRxiv2021

Pyrimidine biosynthesis inhibitors synergize with nucleoside analogs to block SARS-CoV-2 infection

The ongoing COVID-19 pandemic has highlighted the dearth of approved drugs to treat viral infections, with only [~]90 FDA approved drugs against human viral pathogens. To identify drugs that can block SARS-CoV-2 replication, extensive drug screening to repurpose approved drugs is underway. Here, we screened [~]18,000 drugs for antiviral activity using live virus infection in human respiratory cells. Dose-response studies validate 122 drugs with antiviral activity and selectivity against SARS-CoV-2. Amongst these drug candidates are 16 nucleoside analogs, the largest category of clinically used antivirals. This included the antiviral Remdesivir approved for use in COVID-19, and the nucleoside Molnupirivir, which is undergoing clinical trials. RNA viruses rely on a high supply of nucleoside triphosphates from the host to efficiently replicate, and we identified a panel of host nucleoside biosynthesis inhibitors as antiviral, and we found that combining pyrimidine biosynthesis inhibitors with antiviral nucleoside analogs synergistically inhibits SARS-CoV-2 infection in vitro and in vivo suggesting a clinical path forward.

microbiology↗

bioRxiv2021

Distinct movement patterns generate stages of spider web-building

The geometric complexity and stereotypy of spider webs have long generated interest in their algorithmic origin. Like other examples of animal architecture, web construction is the result of several assembly phases that are driven by distinct behavioral stages coordinated to build a successful structure. Manual observations have revealed a range of sensory cues and movement patterns used during web construction, but methods to systematically quantify the dynamics of these sensorimotor patterns are lacking. Here, we apply an analytical pipeline to quantify web-making behavior of the orb-weaver Uloborus diversus. Position tracking revealed stereotyped stages of construction that could occur in typical or atypical progressions across individuals. Using an unsupervised clustering approach, we identified general and stage-specific leg movements. A Hierarchical Hidden Markov Model revealed that stages of web-building are characterized by stereotyped sequences of actions largely shared across individuals, regardless of whether these stages progress in a typical or atypical fashion. Web stages could be predicted based on action-sequences alone, revealing that web-stages are a physical manifestation of underlying behavioral phases. HighlightsO_LISpider centroid trajectories indicate stereotyped progression of web-building stages. C_LIO_LIUnsupervised movement clustering reveals a shared set of movements which correspond to previously defined behaviors that define web-making across individuals. C_LIO_LIStages of web-building use both stage-specific and non-specific behaviors. C_LIO_LIStereotyped and distinct action sequences are predictive of stages of web-building. C_LI

animal behavior and cognition↗

bioRxiv2021

The FDA-approved drug apremilast suppresses alcohol intake: clinical and pre-clinical validation

Treatment options for Alcohol Use Disorders (AUD) have minimally advanced since 2004, while the annual deaths and economic toll have become alarmingly high. Bringing potential therapeutics beyond the bench and into the clinic for AUD requires rigorous pharmacological screening across molecular, behavioral, pre-clinical, and clinical studies in neuroscience. The repurposing of FDA-approved compounds is an effective and expedited means of screening pharmacotherapies for AUD. Here, we demonstrate that apremilast, a phosphodiesterase type 4 inhibitor that is FDA approved for psoriasis and psoriatic arthritis, reduces binge-like alcohol intake and behavioral measures of motivation in unique, preclinical genetic risk models for drinking to intoxication and reduces excessive alcohol drinking in models of stress-facilitated drinking and alcohol dependence. In a double blind, placebo-controlled human laboratory study in non-treatment seeking individuals with AUD, apremilast significantly reduced the number of drinks per day. Lastly, using site-directed drug infusions and electrophysiology we determined that apremilast may act by increasing neural activity in the nucleus accumbens, an important alcohol-related brain region, to reduce alcohol intake in mice. These results demonstrate that apremilast reduces excessive alcohol drinking across a spectrum of AUD severity and support its importance as a potential therapeutic for AUD.

animal behavior and cognition↗

bioRxiv2021

Modeling SARS-CoV-2 and Influenza Infections and Antiviral Treatments in Human Lung Epithelial Tissue Equivalents

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third coronavirus in less than 20 years to spillover from an animal reservoir and cause severe disease in humans. High impact respiratory viruses such as pathogenic beta-coronaviruses and influenza viruses, as well as other emerging respiratory viruses, pose an ongoing global health threat to humans. There is a critical need for physiologically relevant, robust and ready to use, in vitro cellular assay platforms to rapidly model the infectivity of emerging respiratory viruses and discover and develop new antiviral treatments. Here, we validate in vitro human alveolar and tracheobronchial tissue equivalents and assess their usefulness as in vitro assay platforms in the context of live SARS-CoV-2 and influenza A virus infections. We establish the cellular complexity of two distinct tracheobronchial and alveolar epithelial air liquid interface (ALI) tissue models, describe SARS-CoV-2 and influenza virus infectivity rates and patterns in these ALI tissues, the viral-induced cytokine production as it relates to tissue-specific disease, and demonstrate the pharmacologically validity of these lung epithelium models as antiviral drug screening assay platforms.

microbiology↗

bioRxiv2021

Mutations in conserved residues of the myosin chaperone UNC-45 result in both reduced stability and chaperoning activity

Proper muscle development and function depends on myosin being properly folded and integrated into the thick filament structure. For this to occur the myosin chaperone UNC-45, or UNC-45B, must be present and able to chaperone myosin. Here we use a combination of in vivo C. elegans experiments and in vitro biophysical experiments to analyze the effects of six missense mutations in conserved regions of UNC-45/UNC-45B. We found that the phenotype of paralysis and disorganized thick filaments in 5/6 of the mutant nematode strains can likely be attributed to both reduced steady state UNC-45 protein levels and reduced chaperone activity. Interestingly, the biophysical assays performed on purified proteins show that all of the mutations result in reduced myosin chaperone activity but not overall protein stability. This suggests that these mutations only cause protein instability in the in vivo setting and that these conserved regions may be involved in UNC-45 protein stability/ regulation via post translational modifications, protein-protein interactions, or some other unknown mechanism.

molecular biology↗

bioRxiv2020

Creation and validation of 3D-printed head molds for stereotaxic injections of neonatal mouse brains

BackgroundAn increasing number of rodent model systems use injection of DNA or viral constructs in the neonatal brain. However, approaches for reliable positioning and stereotaxic injection at this developmental stage are limited, typically relying on handheld positioning or molds that must be re-aligned for use in a given laboratory. New methodA complete protocol and open source software pipeline for generating 3D-printed head molds derived from a CT scan of a neonatal mouse head cast, together with a universal adapter that can be placed on a standard stereotaxic stage. ResultsA series of test injections with adenovirus encoding red fluorescent protein were conducted using original clay molds and newly generated 3D printed molds. Several metrics were used to compare spread and localization of targeted injections. Comparison with existing methodsThe new method of head mold generation gave comparable results to the field standard, but also allowed the rapid generation of additional copies of each head mold with standardized positioning of the head each time. ConclusionsThis 3D printing pipeline can be used to rapidly develop a series of head molds with standardized injection coordinates across multiple laboratories. More broadly, this pipeline can easily be adapted to other perinatal ages or species.

neuroscience↗

bioRxiv2020

Structure-guided microbial targeting of antistaphylococcal prodrugs

Carboxy ester prodrugs have been widely employed as a means to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can successfully mask problematic chemical features that prevent cellular uptake and can be used to target delivery of compounds to specific tissues. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, curbing their potential therapeutic applications. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes due to a paucity of information about the selectivity of microbial esterases. Here we identify the bacterial esterases, GloB and FrmB, that are required for carboxy ester prodrug activation in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, which revealed several promoieties likely to be serum esterase-resistant while still being microbially labile. These studies lay the groundwork for structure-guided design of anti-staphyloccal promoieties and expand the range of molecules to target staphyloccal pathogens.

biochemistry↗

bioRxiv2020

Spatially localized cluster solutions in inhibitory neural networks

Neurons in the inhibitory network of the striatum display cell assembly firing patterns which recent results suggest may consist of spatially compact neural clusters. Previous computational modeling of striatal neural networks has indicated that non-monotonic, distance-dependent coupling may promote spatially localized cluster firing. Here, we identify conditions for the existence and stability of cluster firing solutions in which clusters consist of spatially adjacent neurons in inhibitory neural networks. We consider simple non-monotonic, distance-dependent connectivity schemes in weakly coupled 1-D networks where cells make strong connections with their kth nearest neighbors on each side. Using the phase model reduction of the network system, we prove the existence of cluster solutions where neurons that are spatially close together are also synchronized in the same cluster, and find stability conditions for these solutions. Our analysis predicts the long-term behavior for networks of neurons, and we confirm our results by numerical simulations of biophysical neuron network models. Additionally, we add weaker coupling between closer neighbors as a perturbation to our network connectivity. We analyze the existence and stability of cluster solutions of the perturbed network and validate our results with numerical simulations. Our results demonstrate that an inhibitory network with non-monotonic, distance-dependent connectivity can exhibit cluster solutions where adjacent cells fire together.

neuroscience↗

bioRxiv2020

The malaria metabolite HMBPP does not trigger erythrocyte terpene production

Infection with malarial parasites renders hosts more mosquito attractive than their uninfected, healthy, counterparts. One volatile organic compound, -pinene, is associated with Plasmodium spp. infection in multiple studies and is a known mosquito attractant. However, how malarial infection results in elevated levels of host-associated -pinene remains unclear. One study suggests that erythrocyte exposure to the malarial metabolite, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), results in increased levels of -pinene. Here, we establish that endogenous levels of -pinene are present in human erythrocytes, that these levels vary widely by erythrocyte donor, and that -pinene levels are not altered by HMBPP treatment.

biochemistry↗