2,427 research outputs found
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Sequencing Technologies in Virology: Advancing Pathogen Detection and Understanding Viral-Host Interactions in Human Retinal Organoids
No full textIn virology, the emergence of sequencing technologies has revolutionized our understanding of viral genetics and epidemiology, marking a significant advancement over traditional methods. These techniques provide deep insights into virus genetics, crucial in addressing the challenges of pathogen detection in public health, such as identifying novel pathogens and monitoring rapid viral mutations that can evade current treatments.This work highlights the crucial role of sequencing as a tool for studying virology, demonstrated through two distinct research approaches. Firstly, we address the challenge posed by the emergence of the SARS-CoV-2 Omicron variant in 2021, which led to a global surge of cases. To identify the introduction of novel SARS-CoV-2 variants in Santa Barbara County, sequencing data was utilized to develop a quantitative reverse transcription PCR-based assay (RT-qPCR), targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 genomes. This assay, tested on 270 clinical samples from Santa Barbara County, accurately and quickly detected the presence of Omicron variants, showing complete concordance with whole viral genome sequencing. The study demonstrates that by utilizing sequencing data to develop RT-qPCR assays offer a rapid and cost-effective solution for virus variant-specific detection, streamlining the identification of Omicron variants in clinical samples.
Secondly, the thesis explores the retinal impact of viral infections, focusing on Zika Virus (ZIKV) and Herpes Simplex Virus 1 (HSV1) interactions with human retinal organoids (ROs) using single-cell RNA sequencing (scRNA-seq). The research reveals that early-stage ROs are broadly susceptible to ZIKV, with a robust upregulation of interferon-stimulated genes and the unfolded protein response, suggesting a dynamic cellular defense. In contrast, HSV1 infection in mature ROs suppresses innate immune responses and reduces transcriptomic diversity, indicating distinct viral pathogenesis mechanisms. These findings, unveiled through scRNA-seq, provide crucial insights into the unique mechanisms of ZIKV and HSV1 in the retina, highlighting the value of retinal organoids in ocular virology research and advancing our understanding of viral pathogenesis in sensory organs.
Together, these studies underscore the versatility and efficacy of sequencing technologies in virological research, from rapid pathogen detection and variant identification to understanding complex interactions in viral pathogenesis, thereby informing public health strategies and potential therapeutic interventions
The Study of Music Therapy: Current Issues and Concepts (Kenneth S. Aigen)
No full textThis is a review of the book "The Study of Music Therapy: Current Issues and Concepts" authored by Kenneth S. Aigen.
Title: The Study of Music Therapy: Current Issues and Concepts | Author: Kenneth S. Aigen | Publication year: 2014 | Publisher: Routledge | Pages: 280 | ISBN: 978-041562641
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The influence of demographic history on the genetics of neurodegenerative illnesses in Colombia
No full textHigh throughput genomic technologies have radically changed the way we understand the genetic landscape of disease. As the field of genomic medicine is growing exponentially, challenges like “lack of transferability" of genetic studies (such as polygenic risk scores) between populations arise. One of the main reasons for this issue, is that recent evolutionary history has created differences in the genetic architecture for disease between human populations. As an example, rare variants show higher geographic clustering and tend to be population-specific. Linkage disequilibrium structure and haplotype blocks around common variants are affected by demographic history as well. One way to circumvent this obstacle is to incorporate diverse populations into genetics studies. Admixed cohorts have proven to be particularly valuable to identify genetic risk for illnesses that are stratified between ancestral origins. This dissertation presents a series of genomic analyses on Colombian individuals with neurodegenerative diseases. We demonstrate that the demographic history of this population affected the genetic burden for neurological disorders, and that by studying individuals with genetic forms of these diseases, we can expand our understanding of the genetic basis of neurodegeneration.The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders and enslaved Africans, all of whom passed through a population bottleneck due to widespread infectious diseases that left small isolated local settlements. As a result, the current population reflects multiple founder effects derived from diverse ancestors. We performed whole genome sequencing in a large cohort of Colombian individuals with Alzheimer’s disease (AD), frontotemporal lobar degeneration-motoneuron disease continuum, early onset dementia and healthy participants. We analyzed their global and local ancestry proportions and screened this cohort for deleterious variants in disease-causing and risk-conferring genes. Then, we present a deeper analysis of one of the families with genetic AD due to a novel variant in PSEN1 (Ile416Thr) of African origin. We describe the phenotype of the symptomatic carriers, as well as their brain accumulation of amyloid-beta and Tau prior to disease onset. Lastly, we explore genetic modifiers of the age at onset for dementia in a large family with autosomal dominant AD due to PSEN1 Glu280Ala. We performed a classic whole genome association study and a novel approach for genetic association using a package that performs a likelihood ratio test with a linear mixed model to adjust for relatedness between individuals. The genomes revealed multiple rare mutations associated with various forms of adult onset familial dementias. Most of these mutations originated from founders and, remarkably, when the entire founder set of mutations was considered together, the genetic consequences of the local demographic histories emerged. In addition, we identified dozens of genome-wide significant loci that modified the age at onset for AD in the Glu280Ala kindred. We also observed a substantial number of individuals with an age of onset well beyond the typical age of onset for this kindred, some of which had high impact coding variants with effect sizes similar to the APOE Christchurch variant (Arg154Ser) recently described in another study.The results here reveal an unexpected genetic richness in a large Colombian cohort selected for the presence of neurodegenerative conditions affecting cognition. Our results suggests that the demographic history of Colombia is likely to underlie the modern clustering of familial neurodegenerative diseases arising from multi-ancestral rare disease-associated alleles. It additionally reinforces the value of these large families with genetic neurodegenerative diseases as platforms for genetic discovery. This set is to our knowledge the largest published study in the literature of the genetics of dementia in a Hispanic descent population. Furthermore, this dissertation underscores the numerous insights that can emerge from Latin American population and the importance of inclusiveness in future genetic studies
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Uncovering the Role of Progranulin in Human iPSC-Derived Microglia and Cerebral Organoids
No full textLoss-of-function mutations in the granulin (GRN) gene cause frontotemporal dementia (FTD) in heterozygosity and neuronal ceroid lipofuscinosis (NCL), a lysosomal storage disease, in homozygosity. While it is well established that disease-causing GRN mutations decrease progranulin (PGRN) levels, leading to neurodegeneration, the cellular and molecular mechanisms underlying these conditions remain poorly understood. To investigate the impact of complete PGRN deficiency in human brain cells, we conducted two separate studies using two disease models: human induced pluripotent stem cell (iPSC)-derived forebrain organoids and microglia.Forebrain organoids allowed us to probe the effects of PGRN deficiency on neuronal and glial cell populations. By employing single-cell RNA sequencing, we uncovered robust downregulation of the mitochondrial oxidative phosphorylation pathway in PGRN KO organoids. In alignment with these results, PGRN loss led to reduced mitochondrial respiration. Additionally, we demonstrated that PGRN KO organoids showed increased levels of reactive oxygen species and exhibited key hallmarks of ferroptosis, including increased lipid peroxidation and iron accumulation. Finally, we showed that PGRN loss leads to increased susceptibility to ferroptotic cell death.
In the second study, we explored the role of PGRN in human iPSC-derived microglia, a cell type absent in forebrain organoids. By integrating transcriptomic and lipidomic analyses, we revealed that PGRN plays a pivotal role in microglial lipid metabolism. PGRN KO microglia showed accumulation of triacylglycerides (TAGs) at baseline and after activation by lipopolysaccharide (LPS) exposure. Interestingly, the lipidomic profiles of resting and activated PGRN KO was distinct, with resting microglia showing a trend for enrichment of TAGs with saturated and monounsaturated long-chain fatty acids, and LPS-treated microglia showing accumulation of TAGs with very long chain polyunsaturated fatty acids. Moreover, we showed that PGRN loss leads to accumulation of lipid droplets. Transcriptomic analysis revealed that PGRN deficient microglia showed dysregulated expression of genes related to lipid metabolism, and our results suggest that PGRN loss drives lipid accumulation by inducing metabolic changes toward increased lipid synthesis and decreased lipid β-oxidation.
Our findings suggest a critical role of mitochondrial dysfunction and impaired responses to oxidative stress in driving neurodegeneration associated with PGRN deficiency, and indicate an important role of PGRN in regulating microglial function and lipid metabolism
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Molecular studies of factors contributing to changes in cellular homeostasis and development of analytical approaches to probe neuronal networks
No full textCellular responses to external stimuli include but are not limited to changes in messenger RNA (mRNA) expression, morphological changes, and alteration to physiological processes. Understanding these basic processes in normal and pathological settings has been an overarching goal of modern biology for the past century. The introduction of modern molecular techniques has led scientists to investigate the structure – function relationship between the fundamental cellular building blocks, proteins and nucleic acids, in an attempt to understand disease states and to be able to treat underlying causes of disease rather than generic symptoms. Continual advances in technology have allowed scientists to design increasingly complex experiments and the application of statistical analyses to large datasets has ushered in a new “-omics” era of biology. Technologies such as next-generation sequencing, single-cell experimentation, and high-resolution arrays for probing neuronal physiology were being introduced to the general scientific community as I was beginning my doctoral studies. Here, over the course of 3 different projects I make use of these advancements to understand the molecular mechanisms underlying cellular responses to different environments and I help to develop novel analytical approaches for probing biological neuronal networks. In the first part, we used an unbiased approach for capturing the expression profile of messenger RNA (mRNA) of bulk cellular samples, RNA sequencing (RNAseq), in order to uncover the molecular responses that take place when a cell recovers from apoptosis, a process termed anastasis. In collaboration with Dr. Denise Montell’s lab, I performed a statistical analysis of gene expression data and found that as cells undergo anastasis their transcriptional profile is actively regulated such that different biological process are being turned on and off as cells recover from apoptosis. This active response was broken down into early and late stages. Early stages represent cells that are transitioning from growth arrested to a proliferation state. In late stages, cells transition from proliferation to a migratory state. In the second project, a collaboration with the laboratory of Dr. Li Gan, we explore how gender contributes to differences in disease phenotypes using wild type mice and transgenic mouse models of neurodegenerative disease. Making use of high-throughput sequencing methods, including microRNA (miRNA) sequencing, bulk RNAseq and single-cell RNA sequencing, we untangle a complex set of interactions that partially explains phenotypic differences between female and male in terms of disease progression as it relates to the microtubule associated protein Tau. Specifically, analysis of the miRNA expression profiles in microglia were different between female and male and when the effect of miRNA was abolished by knocking out a key miRNA processing enzyme, a clear pathogenic difference was observed between male and female with male brains showing greater extent of pathogenesis. Finally, in the 4th chapter of this thesis we develop and test a method for detecting spiking relationships between individual neurons that resembles synaptically coupled neurons in-vitro. We utilized inherent properties of action potentials (APs) propagating through an axon to automate the detection of single neuron AP activity which we define as propagation signals. We extend this analysis method by using propagation signal activity as reference points to perform a cross-correlation computation to identify downstream neurons with statistical relationships to the upstream propagation signal. We validated these relationships by performing manipulations meant to alter mechanisms regulating synaptic transmission and demonstrated that these relationships behave in a manner consistent with synaptic mechanisms
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Unraveling the Protective Mechanisms of APOE3-Christchurch Astrocytes Against Alzheimer’s Disease
No full textAlzheimer’s Disease (AD) is a complex neurodegenerative disorder characterized by the pathological accumulation of tau protein aggregates and amyloid-beta plaques, neuroinflammation, synaptic dysfunction, and widespread metabolic disturbances, all of which contribute to progressive cognitive decline in patients. Astrocytes, the predominant glial cell type in the brain, play a critical role in maintaining central nervous system (CNS) homeostasis. The APOE3-Christchurch (APOE3-Ch) variant has garnered attention for its protective effects against AD, but its molecular and cellular protection mechanisms remain unclear. This dissertation investigates how APOE3-Ch astrocytes contribute to resilience against AD by focusing on their lipid metabolism, tau uptake, and clearance mechanisms, as well as their transcriptomic responses to tau pathology.This work begins by examining the lipidomic profile of APOE3-Ch astrocytes. Although APOE3-Ch astrocytes exhibit lipid dyshomeostasis, including reduced APOE secretion and altered lipid droplet dynamics, they uniquely display lower levels of pathological lipids such as ceramides. These adaptations likely reduce susceptibility to neuroinflammation and mitochondrial dysfunction associated with ceramide accumulation, suggesting a protective lipidomic profile.Next, we investigate the mechanisms underlying tau uptake in APOE3-Ch astrocytes. These cells demonstrate enhanced tau internalization compared to WT astrocytes, mediated through both HSPG and LRP1 pathways. Notably, APOE3-Ch astrocytes exhibit higher HSPG expression, potentially explaining their increased capacity for tau uptake.Further investigations reveal that APOE3-Ch astrocytes achieve more efficient tau degradation, primarily through robust engagement of lysosomal pathways. Lysosomal degradation is activated more rapidly in APOE3-Ch astrocytes. Inhibition studies indicate that while proteasomal pathways contribute to tau degradation in both WT and APOE3-Ch astrocytes, lysosomal pathways are uniquely prominent in APOE3-Ch astrocytes. These findings underscore the enhanced tau clearance capabilities of APOE3-Ch astrocytes and their potential neuroprotective role.Finally, we highlight the genotype-specific transcriptomic program of APOE3-Ch astrocytes in response to tau exposure, including the upregulation of genes involved in cell projection assembly and endocytosis. These adaptations enhance the astrocytes’ ability to internalize and degrade extracellular tau aggregates, further supporting their protective phenotype.In summary, this dissertation elucidates novel molecular and cellular mechanisms underlying the protective properties of APOE3-Ch astrocytes. Their distinct lipidomic profile, enhanced tau uptake and clearance mechanisms, and adaptive transcriptomic responses position APOE3-Ch astrocytes as critical modulators of AD pathology. These findings provide valuable insights into astrocyte-targeted therapeutic strategies, paving the way for future interventions to mitigate tauopathy and neurodegeneration in Alzheimer’s Disease
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Mining Patterns and Networks from Sequence Data
No full textSequence data are ubiquitous in diverse domains such as bioinformatics, computational neuroscience, and user behavior analysis. As a result, many critical applications require extracting knowledge from sequences in multi-level. For example, mining frequent patterns is the central goal of motif discovery in biological sequences, while in computational neuronal science, one essential task is to infer causal networks from neural event sequences (spike trains). Given the wide application of pattern and network mining tools for sequence data, they are facing new challenges posted by modern instruments. That is, as large scale and high resolution sequence data become available, we need new methods with better efficiency and higher accuracy.In this dissertation, we propose several approaches to improve existing pattern and network mining tools to meet new challenges in terms of efficiency and accuracy. The first problem is how to scale existing motif discovery algorithms. Our work on motif discovery focuses on the challenge of discovering motifs from a large scale of short sequences that none of existing motif finding algorithms can handle. We propose an anchor based clustering algorithm that could significantly improve the scalability of all the existing motif finding algorithms without losing accuracy at all. In particular, our algorithm could reduce the running time of a very popular motif finding algorithm, MEME, from weeks to a few minutes with even better accuracy.In another work, we study the problem of how to accurately infer a functional network from neural recordings (spike trains), which is an essential task in many real world applications such as diagnosing neurodegenerative diseases. We introduce a statistical tool that could be used to accurately identify inhibitory causal relations from spike trains. While most of existing works devote their efforts on characterizing the statistics of neural spike trains, we show that it is crucial to make predictions about the response of neurons to changes. More importantly, our results are validated by real biological experiments with a novel instrument, which makes this work the first of its kind. Furthermore, while most existing methods focus on learning functional networks from purely observational data, we propose an active learning framework that could intelligently generate and utilize interventional data. We demonstrate that by intelligently adopting interventional data using the active learning models we propose, the accuracy of the inferred functional network could be substantially improved with the same amount of training data
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Quantifying the extent of horizontal gene transfer in the genomes of Pink Berries
No full textHorizontal Gene Transfer (HGT) refers to sharing of small segments of genetic material from a donor to a recipient organism that does not have a parent-offspring relationship. Although not all transfers are successful, they are still abundant in natural bacterial communities. Moreover, the rate at which a gene is transferred differs widelyacross different genes and organisms. This makes it challenging, especially for healthcare professionals that study antimicrobial resistance and epidemics, to predict how the organism will evolve over time and over environmental fluctuations. Recombination creates more opportunities for a local adaptation by making it possible to acquire genes involved in antibiotic resistance, pathogenic determinants, etc. Many metagenomic studies have used natural biofilms in order to measure the rates of gene transfer across communities. Moreover, not only can one study genes responsible for protection against outside influence or metabolism but metagenomic studies of biofilms and microbial mats can provide invaluable insights into evolutionary processes within natural communities.
In the first chapter a comprehensive analysis of the Pink Berry metagenomic data is performed in context of extensive recombination of a quasi-sexual bacterial population. Evidence is presented showing that the populations are divided into clades with different evolutionary histories including a mixing layer where bacteria experience extensive recombination from other clades as well as with each other.
In the second part of this thesis I focus on self / non-self bacterial recognition. Toxinantitoxin systems are important mechanisms for the bacteria to respond to intracellular stress. Usually, the proteins that are a part of the contact dependent growth inhibition (CDI) secretion contain multiple distinct parts - the structure that acts as a delivery mechanism, the toxin, and the antitoxin. Here the preliminary findings of diversity in WapA and RhsC C-termini in purple sulfur bacteria is shown. The presence of large gaps in the alignment of the C-terminus region of the CDI proteins shows that the
bacteria differ in their repertoire of toxins depending on their geographical location. These observations mark a promising starting point for studying CDI mechanisms in naturally occurring bacterial populations.
Lastly, the composition of bacterial communities grown in different conditions based on their 16S sequences is analyzed. In this chapter I have introduced a new tool for decreasing the error of 16S Nanopore sequences and identifying given samples. The accuracy of the pipeline using simulated PacBio and Nanopore datasets from CAMI2 is
demonstrated and then it is used on experimental sediment data
Life at Low Copy Number: How Dendrites Manage with So Few mRNAs
No full textMost mammalian dendrites have surprisingly few copy numbers of mRNAs relative to the large number of synapses and consequently, at any given moment, the majority of synapses do not have a repertoire of mRNAs within their immediate locale capable of initiating translation-dependent plasticity. The dimensions of the translationally serviceable locale around synapses have boundary parameters that can be estimated. When a synapse receives an input beyond that boundary, the requisite mRNAs for local translation and plasticity may not be there. How a complex dendritic arbor optimizes this paucity of mRNAs opens several functional considerations that are related to the dynamic range of dendritic plasticity, sparse coding, and modifications of firing rates. RNA localization in dendrites may instantiate a neuron's history and establishes a bias toward inputs that synapse on RNA-laden synaptic clusters. Low copy numbers create an element of stochasticity to the induction of translation-dependent plasticity that allows the dendrite opportunities to respond to novel and unexpected inputs
Book Review: Boots and Suits: Historical Cases and Contemporary Lessons in Military Diplomacy
No full textAuthor: Philip S. Kosnett (editor)
Reviewed by Kenneth Weisbrode, assistant professor of history, Bilkent University
Historian and professor Kenneth Weisbrode reviews retired US ambassador Philip S. Kosnett’s anthology on “just how contested, and how significant,” military diplomacy is. After highlighting the value of General Kenneth F. McKenzie’s (US Marine Corps, retired) instructive foreword, which defines military diplomacy, Weisbrode outlines the book’s range of case studies across history (from the Confederacy to Afghanistan), author perspectives (“academics and government officials”), and subject matter (“strategy, operations, and tactics”). He distills some of the book’s essential policy lessons for readers and notes the book’s wide-ranging utility for “teachers, students, and aspiring (or even veteran) military diplomats.”https://press.armywarcollege.edu/parameters_bookshelf/1036/thumbnail.jp
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