Recent studies recognize a vast diversity of noncoding RNAs with largely unknown functions, but few have examined interspersed repeat sequences, which constitute almost half our genome. RNA hybridization in situ using C0T-1 (highly repeated) DNA probes detects surprisingly abundant euchromatin-associated RNA comprised predominantly of repeat sequences (C0T-1 RNA), including LINE-1. C0T-1-hybridizing RNA strictly localizes to the interphase chromosome territory in cis and remains stably associated with the chromosome territory following prolonged transcriptional inhibition. The C0T-1 RNA territory resists mechanical disruption and fractionates with the nonchromatin scaffold but can be experimentally released. Loss of repeat-rich, stable nuclear RNAs from euchromatin corresponds to aberrant chromatin distribution and condensation. C0T-1 RNA has several properties similar to XIST chromosomal RNA but is excluded from chromatin condensed by XIST. These findings impact two "black boxes" of genome science: the poorly understood diversity of noncoding RNA and the unexplained abundance of repetitive elements.
The primary cilium is a sensory organelle, defects in which cause a wide range of human diseases including retinal degeneration, polycystic kidney disease and birth defects. The sensory functions of cilia require specific receptors to be targeted to the ciliary subdomain of the plasma membrane. Arf4 has been proposed to sort cargo destined for the cilium at the Golgi complex and deemed a key regulator of ciliary protein trafficking. In this work, we show that Arf4 binds to the ciliary targeting sequence (CTS) of fibrocystin. Knockdown of Arf4 indicates that it is not absolutely required for trafficking of the fibrocystin CTS to cilia as steady-state CTS levels are unaffected. However, we did observe a delay in delivery of newly synthesized CTS from the Golgi complex to the cilium when Arf4 was reduced. Arf4 mutant mice are embryonic lethal and die at mid-gestation shortly after node formation. Nodal cilia appeared normal and functioned properly to break left-right symmetry in Arf4 mutant embryos. At this stage of development Arf4 expression is highest in the visceral endoderm but we did not detect cilia on these cells. In the visceral endoderm, the lack of Arf4 caused defects in cell structure and apical protein localization. This work suggests that while Arf4 is not required for ciliary assembly, it is important for the efficient transport of fibrocystin to cilia, and also plays critical roles in non-ciliary processes.
Senescence-associated β-galactosidase activity marks the visceral endoderm of mouse embryos but is not indicative of senescence
Senescence-associated β-galactosidase (SA-β-gal) activity is widely used as a marker of cellular senescence and as an indicator of organismal aging. Here, we report that SA-β-gal activity is present in the visceral endoderm layer of early postimplantation mouse embryos in predictable patterns that vary as the embryo progresses in development. However, determination of the mitotic index and analysis of the expression of Cdkn1a (p21), a marker of senescent cells, do not indicate cellular senescence. Instead, analysis of embryos in culture revealed the presence of SA-β-gal activity in apical vacuoles of visceral endoderm cells likely a reflection of acidic β-galactosidase function in these organelles. SA-β-gal serves as a practical marker of the dynamics of the visceral endoderm that can be applied to developmental as well as functional studies of early mammalian embryos.
The Drosophila annotated gene CG5155 encodes a protein that contains 10 Armadillo-repeats and has an unknown function. To fill this gap, we performed loss-of-function studies using RNAi. By analysis of four independent Drosophila RNAi lines targeting two non-overlapping regions of the CG5155 transcript, we demonstrate that this gene is required for male fertility. Therefore, we have named this gene Gudu. The transcript of Gudu is highly enriched in adult testes. Knockdown of Gudu by a ubiquitous driver leads to defects in the formation of the individualization complex that is required for spermatid maturation, thereby impairing spermatogenesis. Furthermore, testis-specific knockdown of Gudu by crossing the RNAi lines with the bam-Gal4 driver is sufficient to cause the infertility and defective spermatogenesis. Since Gudu is highly homologous to vertebrate ARMC4, also an Armadillo-repeat-containing protein enriched in testes, our results suggest that Gudu and ARMC4 are a subfamily of Armadillo-repeat containing proteins that may have an evolutionarily conserved function in spermatogenesis.
Both Glis, the downstream effectors of hedgehog signaling, and Zic transcription factors are required for Myf5 expression in the epaxial somite. Here we demonstrate a novel synergistic interaction between members of both families and Pax3, a paired-domain transcription factor that is essential for both myogenesis and neural crest development. We show that Pax3 synergizes with both Gli2 and Zic1 in transactivating the Myf5 epaxial somite (ES) enhancer in concert with the Myf5 promoter. This synergy is dependent on conserved functional domains of the proteins, as well as on a novel homeodomain motif in the Myf5 promoter and the essential Gli motif in the ES enhancer. Importantly, overexpression of Zic1 and Pax3 in the 10T1/2 mesodermal cell model results in enrichment of these factors at the endogenous Myf5 locus and induction of Myf5 expression. In our previous work, we showed that by enhancing nuclear translocation of Gli factors, Zics provide spatiotemporal patterning for Gli family members in the epaxial induction of Myf5 expression. Our current study indicates a complementary mechanism in which association with DNA-bound Pax3 strengthens the ability of both Zic1 and Gli2 to transactivate Myf5 in the epaxial somite.
The Hedgehog pathway plays important roles in embryonic development, adult stem cell maintenance and tumorigenesis. In mammals these effects are mediated by Sonic, Desert and Indian Hedgehog (Shh, Dhh and Ihh). Shh undergoes autocatalytic cleavage and dual lipidation prior to secretion and forming a response gradient. Post-translational processing and secretion of Dhh and Ihh ligands has not previously been investigated. This study reports on the synthesis, processing, secretion and signaling activities of SHH, IHH and DHH preproteins expressed in cultured cells, providing unexpected evidence that DHH does not undergo substantial autoprocessing or secretion, and does not function in paracrine signaling. Rather, DHH functions as a juxtacrine signaling ligand to activate a cell contact-mediated HH signaling response, consistent with its localised signaling in vivo. Further, the LnCAP prostate cancer cell, when induced to express endogenous DHH and SHH, is active only in juxtacrine signaling. Domain swap studies reveal that the C-terminal domain of HH regulates its processing and secretion. These findings establish a new regulatory role for HHs in cell-mediated juxtacrine signaling in development and cancer.
Development of novel therapeutics requires good animal models of disease. Disorders for which good animal models do not exist have very few drugs in development or clinical trial. Even where there are accepted, albeit imperfect models, the leap from promising preclinical drug results to positive clinical trials commonly fails, including in disorders of skeletal muscle. The main alternative model for early drug development, tissue culture, lacks both the architecture and, usually, the metabolic fidelity of the normal tissue in vivo. Herein, we demonstrate the feasibility and validity of human to mouse xenografts as a preclinical model of myopathy. Human skeletal muscle biopsies transplanted into the anterior tibial compartment of the hindlimbs of NOD-Rag1null IL2rgammanull immunodeficient host mice regenerate new vascularized and innervated myofibers from human myogenic precursor cells. The grafts exhibit contractile and calcium release behavior, characteristic of functional muscle tissue. The validity of the human graft as a model of facioscapulohumeral muscular dystrophy is demonstrated in disease biomarker studies, showing that gene expression profiles of xenografts mirror those of the fresh donor biopsies. These findings illustrate the value of a new experimental model of muscle disease, the human muscle xenograft in mice, as a feasible and valid preclinical tool to better investigate the pathogenesis of human genetic myopathies and to more accurately predict their response to novel therapeutics.
From Neurodegeneration to Infertility and Back - Exploring Functions of Two Genes: ARMC4 and TARDBP: A Dissertation
Amyotrophic Lateral Sclerosis (ALS) is an adult-onset progressive neurodegenerative disease that causes degeneration in both upper and lower motor neurons. ALS progresses relentlessly after the onset of the disease, with most patients die within 3-5 years of diagnosis, largely due to respiratory failure. Since SOD1 became the first gene whose mutations were associated with ALS in 1993, more than 17 ALS causative genes have been identified. Among them, TAR DNA-binding protein (TARDBP) lies in the central of ALS pathology mechanism study, because TDP43 proteinopathy is observed not only in familial ALS cases carrying TARDBP mutations, but also in most of the sporadic ALS cases, which account for 90% of the whole ALS population. Several TDP43 overexpression mouse models have been successfully generated to study the gain-of-toxicity mechanism of TDP43 in ALS development, while the investigation of loss-of-function mechanism which could also contribute to ALS still awaits a proper mouse model. The major difficulty in generating TARDBP knock out mouse model lies in the fact that TARDBP is a development essential gene and complete depletion of TDP43 function causes embryonic lethality.
In chapter I, I reviewed the recent advances in ALS study. Emphasis was given to ALS mouse models, especially TARDBP ALS mouse model.
In Chapter II, I made a Tet-responsive construct that contains mCherry, a fluorescent protein, as an indicator for the expression of the artificial miRNA (amiTDP) residing in the 3’UTR of mCherry and targeting TARDBP. The construct was tested in NSC34 cells and TRE-mCherry-amiTDP43 transgenic mouse was generated with this construct. Crossing TRE-mCherry-amiTDP43 mouse with mPrp-tTA mouse, mCherry expression was successfully induced in mouse forebrain and cerebellum, but not in other tissues including spinal cord. By quantitative real-time PCR, amiTDP43 expression was confirmed to be coupled with mCherry expression. Fluorescent immunostaining revealed that mCherry was expressed in neurons, but not in astrocytes or microglia cells, and that in mCherry positive cells, TDP43 was significantly knocked down. Results from Nissl staining and GFAP immunostaining suggested that decrease of TDP43 in forebrain neuron only was not sufficient to cause neurodegeneration and neuron loss.
In chapter III, I investigated the function of Armadillo Containing Protein 4 (ARMC4), which was originally considered ALS causative gene. Our study of the function of CG5155, the possible homolog of ARMC4 in Drosophila, indicated that CG5155 is a male fertility gene that is involved in spermatogenesis. Therefore, we have named this gene Gudu. The transcript of Gudu is highly enriched in adult testes. Knockdown of Gudu by a ubiquitous driver leads to defects in the formation of the individualization complex that is required for spermatid maturation, thereby impairing spermatogenesis. Furthermore, testis-specific knockdown of Gudu by crossing the RNAi lines with Bam-Gal4 driver is sufficient to cause the infertility and defective spermatogenesis. Since Gudu is highly homologous to vertebrate ARMC4, also an Armadillo-repeat-containing protein enriched in testes, our results suggest that Gudu and ARMC4 is a subfamily of Armadillo-repeat containing proteins with an evolutionarily conserved function in spermatogenesis.
Characterization of the Visceral Endoderm Components in Early Post-Implantation Mouse Embryo Development: A Dissertation
Early post-implantation vertebrate embryos are shaped by complex cellular and molecular mechanisms. In mice, the visceral endoderm, an extraembryonic cell lineage that appears before gastrulation, provides several important functions such as nutrition and mechanical protection. My thesis research focused on the role of the visceral endoderm in embryo patterning, a newly discovered function for this tissue. My results showed that an interplay between two subpopulations of visceral endoderm the anterior and posterior visceral endoderm, located on the opposite sides of the developing conceptus, are critical for the establishment of the anteroposterior body axis of the embryo. I also found that senescence-associated β-galactosidase activity delineates the visceral endoderm marking apical vacuole, a lysosomal-like organelle. This however indicates the nutritional function of visceral endoderm cells rather than a senescent population. My studies highlight the fundamental role of extraembryonic tissues in patterning mammalian embryos as opposed to housekeeping roles. They also reveal important difference when conducting studies at the organismal level rather than in cells in culture.
BACKGROUND: Current guidelines recommend early oral beta-blocker administration in the management of acute coronary syndromes for patients who are not at high risk of complications.
METHODS: Data from patients enrolled between 2000 and 2007 in the Global Registry of Acute Coronary Events (GRACE) were used to evaluate hospital outcomes in three cohorts of patients admitted with ST-elevation myocardial infarction, based on beta-blocker use (early [first 24 hours] intravenous [± oral], only early oral, or delayed [after first 24 hours]).
RESULTS: Among 13,110 patients with a ST-elevation myocardial infarction, 21% received any early intravenous beta-blockers, 65% received only early oral beta-blockers, and 14% received delayed (>24 hours) beta-blockers. Higher systolic blood pressure, higher heart rate, and chronic beta-blocker use were independent predictors of early beta-blocker use. Early beta-blocker use was less likely in older patients, patients with moderate to severe left ventricular dysfunction, and in those presenting with inferior myocardial infarction or Killip class III heart failure. Intravenous beta-blocker use and delayed beta-blocker use were associated with higher rates of cardiogenic shock, sustained ventricular fibrillation/ventricular tachycardia and acute heart failure, compared with oral beta-blocker use. In-hospital mortality was increased with IV beta-blocker use (propensity score adjusted odds ratio [OR] 1.41; 95% confidence interval [CI], 1.03-1.92) but significantly reduced with delayed beta-blocker administration (propensity adjusted OR, 0.44; 95% CI, 0.26-0.74).
CONCLUSIONS: Early beta-blocker use is common in patients presenting with ST-elevation myocardial infarction, with oral administration being most prevalent. Oral beta-blockers were associated with a decrease in the risk of cardiogenic shock, ventricular arrhythmias, and acute heart failure. However, the early receipt of any form of beta-blockers was associated with an increase in hospital mortality.
Wireless body area networks (WBANs) are cyber-physical systems that emerged as a key technology to provide real-time health monitoring and ubiquitous healthcare services. WBANs could operate in dense environments such as in a hospital and lead to a high mutual communication interference in many application scenarios. The excessive interferences will significantly degrade the network performance, including depleting the energy of WBAN nodes more quickly and even eventually jeopardize people's lives because of unreliable (caused by the interference) healthcare data collections. Therefore, it is critical to mitigate the interference among WBANs to increase the reliability of the WBAN system while minimizing the system power consumption. Many existing approaches can deal with communication interference mitigation in general wireless networks but are not suitable for WBANs because of ignoring the social nature of WBANs by them. Unlike the previous research, we for the first time propose a power game based approach to mitigate the communication interferences for WBANs based on the people's social interaction information. Our major contributions include: 1) modeling the inter-WBANs interference and determine the distance distribution of the interference through both theoretical analysis and Monte Carlo simulations; 2) developing social interaction detection and prediction algorithms for people carrying WBANs; and 3) developing a power control game based on the social interaction information to maximize the system's utility while minimize the energy consumption of WBANs system. The extensive simulation results show the effectiveness of the power control game for inter-WBAN interference mitigation using social interaction information. Our research opens a new research vista of WBANs using social networks.
Increasing population density, closer social contact, and interactions make epidemic control difficult. Traditional offline epidemic control methods (e.g., using medical survey or medical records) or model-based approach are not effective due to its inability to gather health data and social contact information simultaneously or impractical statistical assumption about the dynamics of social contact networks, respectively. In addition, it is challenging to find optimal sets of people to be isolated to contain the spread of epidemics for large populations due to high computational complexity. Unlike these approaches, in this paper, a novel cluster-based epidemic control scheme is proposed based on Smartphonebased body area networks. The proposed scheme divides the populations into multiple clusters based on their physical location and social contact information. The proposed control schemes are applied within the cluster or between clusters. Further, we develop a computational efficient approach called UGP to enable an effective cluster-based quarantine strategy using graph theory for large scale networks (i.e., populations). The effectiveness of the proposed methods is demonstrated through both simulations and experiments on real social contact networks.
Our goal in the present study was to examine the effects of maternal smoking during pregnancy on infant self-regulation, exploring birth weight as a mediator and sex as a moderator of risk. A prospective sample of 218 infants was assessed at 6 months of age. Infants completed a battery of tasks assessing working memory/inhibition, attention, and emotional reactivity and regulation. Propensity scores were used to statistically control for confounding risk factors associated with maternal smoking during pregnancy. After prenatal and postnatal confounds were controlled, prenatal tobacco exposure was related to reactivity to frustration and control of attention during stimulus encoding. Birth weight did not mediate the effect of prenatal exposure but was independently related to reactivity and working memory/inhibition. The effect of tobacco exposure was not moderated by sex. (PsycINFO Database Record (c) 2014 APA, all rights reserved).
Published as Chapter 10 "Research Data Management and the Health Sciences Librarian" in Health Sciences Librarianship edited by M. Sandra Wood. Chicago: Rowman & Littlefield and the Medical Library Association, 2014. Link to book on publisher's website.
All rights reserved by the publishers. PDF of book chapter posted with publisher's permission.
The importance of the human microbiome in health may be the single most valuable development in our conception of the microbial world since Pasteur's germ theory of the 1860s. Its implications for our understanding of health and pathogenesis are profound. Coupled with the revolution in diagnostics that we are now witnessing - a revolution that changes medicine from a science of symptoms to a science of causes - we cannot continue to develop antibiotics as we have for the past 80 years. Instead, we need to usher in a new conception of the role of antibiotics in treatment: away from single molecules that target broad phylogenetic spectra and towards targeted molecules that cripple the pathogen while leaving the rest of the microbiome largely intact.
Parental mastery of continuous subcutaneous insulin infusion skills and glycemic control in youth with type 1 diabetes
OBJECTIVE: The purpose of this study is to determine whether parental knowledge of the continuous subcutaneous insulin infusion (CSII) device affects glycemic control as measured by hemoglobin A1c (A1C) level.
SUBJECTS AND METHODS: Parents of children with type 1 diabetes mellitus (T1DM) using CSII completed a 14-item questionnaire. Questions 1-10 were knowledge-based questions that required the parent to extract specific information from their child's CSII device. Questions 11-14 asked parents to provide a self-assessment of their CSII knowledge.
RESULTS: Twenty-two parents of youth with T1DM participated in the study. Ten of the youth were in the Low-A1C group (A1C/=8%). Parents of youth in the Low-A1C group scored statistically better on the 10-item performance survey than parents of youth in the High-A1C group. Most of the parents of children in the Low-A1C group responded that they knew their child's insulin pump "very well" and that their pump knowledge had "increased" since their child started on the insulin pump.
CONCLUSIONS: Our findings reveal that youth with T1DM whose parents are more knowledgeable about pump functions have optimal glycemic control as evidenced by A1C. These findings underscore the importance of ongoing pump training for both pediatric patients and their parents.
Point process modeling of interbreath interval: a new approach for the assessment of instability of breathing in neonates
Interbreath interval (IBI), the time interval between breaths, is an important measure used to analyze irregular breathing patterns in neonates. The discrete bursts of neural activity generate the IBI time series, which exhibits stochastic as well as deterministic dynamics. To quantify the irregularity of breathing, we propose a point process model of IBI using a comprehensive stochastic dynamic modeling framework. The IBIs of immature breathing patterns exhibit a long tail distribution and within a point process model, we have considered the lognormal distribution to represent the stochastic IBI characteristics. An autoregressive (AR) function is embedded within the model to capture the short-term IBI dynamics including abrupt IBI prolongations related to sporadic and periodic apneas that are common in neonates. We tested the utility of our paradigm for depicting the respiratory dynamics in neonatal rats and in preterm infants. Kolmogorov-Smirnov (KS) and independence tests reveal that the model accurately tracks the dynamic characteristics of the signals. In preterm infants, our model-derived indices of IBI instability strongly correlate with clinically derived indices of maturation. Our results validate a new class of algorithms, based on the point process theory, for defining instantaneous measures of breathing irregularity in neonates.
Human Treg responses allow sustained recombinant adeno-associated virus-mediated transgene expression
Recombinant adeno-associated virus (rAAV) vectors have shown promise for the treatment of several diseases; however, immune-mediated elimination of transduced cells has been suggested to limit and account for a loss of efficacy. To determine whether rAAV vector expression can persist long term, we administered rAAV vectors expressing normal, M-type alpha-1 antitrypsin (M-AAT) to AAT-deficient subjects at various doses by multiple i.m. injections. M-specific AAT expression was observed in all subjects in a dose-dependent manner and was sustained for more than 1 year in the absence of immune suppression. Muscle biopsies at 1 year had sustained AAT expression and a reduction of inflammatory cells compared with 3 month biopsies. Deep sequencing of the TCR Vbeta region from muscle biopsies demonstrated a limited number of T cell clones that emerged at 3 months after vector administration and persisted for 1 year. In situ immunophenotyping revealed a substantial Treg population in muscle biopsy samples containing AAT-expressing myofibers. Approximately 10% of all T cells in muscle were natural Tregs, which were activated in response to AAV capsid. These results suggest that i.m. delivery of rAAV type 1-AAT (rAAV1-AAT) induces a T regulatory response that allows ongoing transgene expression and indicates that immunomodulatory treatments may not be necessary for rAAV-mediated gene therapy.
Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells
The identification of the trans-acting factors and cis-regulatory modules that are involved in human pluripotent stem cell (hPSC) maintenance and differentiation is necessary to dissect the operating regulatory networks in these processes and thereby identify nodes where signal input will direct desired cell fate decisions in vitro or in vivo. To deconvolute these networks, we established a method to influence the differentiation state of hPSCs with a CRISPR-associated catalytically inactive dCas9 fused to an effector domain. In human embryonic stem cells, we find that the dCas9 effectors can exert positive or negative regulation on the expression of developmentally relevant genes, which can influence cell differentiation status when impinging on a key node in the regulatory network that governs the cell state. This system provides a platform for the interrogation of the underlying regulators governing specific differentiation decisions, which can then be employed to direct cellular differentiation down desired pathways.
Relation between soluble ST2, growth differentiation factor-15, and high-sensitivity troponin I and incident atrial fibrillation
BACKGROUND: We investigated whether circulating concentrations of soluble ST2, growth differentiation factor-15 (GDF-15), and high-sensitivity troponin I (hsTnI) are associated with incident atrial fibrillation (AF) and whether these biomarkers improve current risk prediction models including AF risk factors, B-type natriuretic peptide (BNP), and C-reactive protein (CRP).
METHODS: We studied the relation between soluble ST2, GDF-15, and hsTnI and development of AF in Framingham Heart Study participants without prevalent AF. We used Cox proportional hazard regression analysis to examine the relation of incident AF during a 10-year follow-up period with each biomarker. We adjusted for standard AF clinical risk factors, BNP, and CRP.
RESULTS: The mean age of the 3,217 participants was 59 +/- 10 years, and 54% were women. During a 10-year follow-up, 242 participants developed AF. In age- and sex-adjusted models, GDF-15 and hsTnI were associated with risk of incident AF; however, after including the AF risk factors and BNP and CRP, only hsTnI was significantly associated with AF (hazard ratio per 1 SD of loge hsTnI, 1.12, 95% CI 1.00-1.26, P = .045). The c statistic of the base model including AF risk factors, BNP, and CRP was 0.803 (95% CI 0.777-0.830) and did not improve by adding individual or all 3 biomarkers. None of the discrimination and reclassification statistics were significant compared with the base model.
CONCLUSION: In a community-based cohort, circulating hsTnI concentrations were associated with incident AF. None of the novel biomarkers evaluated improved AF risk discrimination or reclassification beyond standard clinical AF risk factors and biomarkers.