A Human Torque Teno Virus Encodes a MicroRNA That Inhibits Interferon Signaling

Rodney P. Kincaid, James M. Burke, Jennifer C. Cox, Christopher S. Sullivan, The University of Texas at Austin, Molecular Genetics and Microbiology, Austin, Texas, United States of AmericaEthel-Michele de Villiers, Division for the Characterization of Tumorviruses, Deutsches Krebsforschungszentrum, Heidelberg, GermanyTorque teno viruses (TTVs) are a group of viruses with small, circular DNA genomes. Members of this family are thought to ubiquitously infect humans, although causal disease associations are currently lacking. At present, there is no understanding of how infection with this diverse group of viruses is so prevalent. Using a combined computational and synthetic approach, we predict and identify miRNA-coding regions in diverse human TTVs and provide evidence for TTV miRNA production in vivo. The TTV miRNAs are transcribed by RNA polymerase II, processed by Drosha and Dicer, and are active in RISC. A TTV mutant defective for miRNA production replicates as well as wild type virus genome; demonstrating that the TTV miRNA is dispensable for genome replication in a cell culture model. We demonstrate that a recombinant TTV genome is capable of expressing an exogenous miRNA, indicating the potential utility of TTV as a small RNA vector. Gene expression profiling of host cells identifies N-myc (and STAT) interactor (NMI) as a target of a TTV miRNA. NMI transcripts are directly regulated through a binding site in the 3′UTR. SiRNA knockdown of NMI contributes to a decreased response to interferon signaling. Consistent with this, we show that a TTV miRNA mediates a decreased response to IFN and increased cellular proliferation in the presence of IFN. Thus, we add Annelloviridae to the growing list of virus families that encode miRNAs, and suggest that miRNA-mediated immune evasion can contribute to the pervasiveness associated with some of these viruses.This work was supported by grants RO1AI077746 from the National Institutes of Health, RP110098 from the Cancer Prevention and Research Institute of Texas, a Burroughs Wellcome Investigators in Pathogenesis Award to CSS, a UT Austin Powers Graduate Fellowship to RPK, a UT Austin Institute for Cellular and Molecular Biology fellowship, and the DKFZ for EMdV. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Molecular BiosciencesMicrobiologyEmail: [email protected]

Creating High Throughput Low Cost Analysis of Different Labor-Intensive Repetitive Research Processes

Many research projects suffer from limited data causing poor statistical analysis or limited results. The movement to high throughput methods has been building for many years and cross many different disciplines. Lots of these methods start out using pathways that generate large amounts of data but have limited methods to process or analyze that data. Most of this data collection and analysis generates tremendous labor and reduces accuracy of input. In this thesis I present two new methods and software tools to help reduce labor and increase the scope of data analysis around high throughput research. These include a method to analyze RNA-Seq data and identify the statistically relevant optimal number of reads needed for the transcriptome analysis. This allows groups to avoid unnecessary excessive number of reads from a given sample and instead opt for increasing the number of samples and/or replicates they can incorporate to an analysis at the same costs. Often the limited costs outweigh the sequencing of adequate number of samples and replicates. The second major high throughput image analysis tool I developed involves automation, machine learning and image processing to score for potential use in object identity and phenotyping. To increase throughput and build consistency over analysis by a human, machine learning methods are used increasingly on a wide array of data types

The Short-Term Dynamics of Peers and Delinquent Behavior: An Analysis of Bi-weekly Changes Within a High School Student Network

_Objectives:_ To analyze short-term changes in peer affiliations, offending behavior and routine activities in order to evaluate three different processes: peer selection, peer socialization an

And the Heat Goes On: Police Repression and the Modalities of Power

Among security institutions, police occupy a unique position. In addition to specializing in the repression of dissent, police monitor society and enforce order. Yet within research studying state repression, how police institutions are used and deployed to control domestic threats remain under-explored, particularly as it relates to the dual functionality just described. In this study, we develop and test an explanation of police repression accounting for the bifurcation of Mann’s two modalities of state power: infrastructural power and despotic power. Infrastructural power allocates police resources to surveil dissidents and preemptively limit dissent’s emergence or escalation. Police deploy despotic power through repressive responses to political threats. Empirically, we employ unique data to investigate police repression and the modalities of power in Guatemala. To analyze how shifting the balance between infrastructural and despotic power affects police repression, we isolate damage occurring from an earthquake that exogenously reshaped the landscape of infrastructural power. Results affirm the role of infrastructural power in regulating the despotic power of the state. Where local infrastructure was most affected by the earthquake, the security apparatus lost the capacity to surveil nascent movements and predict their activity, thereby providing opportunity for dissidents to mobilize and forcing police to (over-)react rather than shutdown resistance preemptively. However, the intensity of state violence recedes as the state recovers from the infrastructural damage and regains its control of local district

Differential regulation of bladder pain and voiding function by sensory afferent populations revealed by selective optogenetic activation

Bladder-innervating primary sensory neurons mediate reflex-driven bladder function under normal conditions, and contribute to debilitating bladder pain and/or overactivity in pathological states. The goal of this study was to examine the respective roles of defined subtypes of afferent neurons in bladder sensation and function in vivo via direct optogenetic activation. To accomplish this goal, we generated transgenic lines that express a Channelrhodopsin-2-eYFP fusion protein (ChR2-eYFP) in two distinct populations of sensory neurons: TRPV1-lineage neurons (Trpv1Cre;Ai32, the majority of nociceptors) and Nav1.8+ neurons (Scn10aCre;Ai32, nociceptors and some mechanosensitive fibers). In spinal cord, eYFP+ fibers in Trpv1Cre;Ai32 mice were observed predominantly in dorsal horn (DH) laminae I-II, while in Scn10aCre;Ai32 mice they extended throughout the DH, including a dense projection to lamina X. Fiber density correlated with number of retrogradely-labeled eYFP+ dorsal root ganglion neurons (82.2% Scn10aCre;Ai32 vs. 62% Trpv1Cre;Ai32) and degree of DH excitatory synaptic transmission. Photostimulation of peripheral afferent terminals significantly increased visceromotor responses to noxious bladder distension (30–50 mmHg) in both transgenic lines, and to non-noxious distension (20 mmHg) in Scn10aCre;Ai32 mice. Depolarization of ChR2+ afferents in Scn10aCre;Ai32 mice produced low- and high-amplitude bladder contractions respectively in 53% and 27% of stimulation trials, and frequency of high-amplitude contractions increased to 60% after engagement of low threshold (LT) mechanoreceptors by bladder filling. In Trpv1Cre;Ai32 mice, low-amplitude contractions occurred in 27% of trials before bladder filling, which was pre-requisite for light-evoked high-amplitude contractions (observed in 53.3% of trials). Potential explanations for these observations include physiological differences in the thresholds of stimulated fibers and their connectivity to spinal circuits

Charting self-esteem during marital dissolution.

ObjectiveThe purpose of this study was to chart changes in self-esteem before and after marital dissolution to identify the factors that shape individuals' self-esteem during this life transition.MethodWe analyzed 10 annual waves of self-esteem data from 291 divorcees from a nationally representative panel study of the Netherlands (N ~ 13,000). We charted the course of self-esteem before and after marital dissolution and tested a broad set of moderator variables that may shape individuals' self-esteem trajectories.ResultsThe average divorcee experienced significant decrease in self-esteem preceding marital dissolution and remained stable afterward. There were substantial individual differences in self-esteem trajectories, both before and after marital separation. Divorcees who experienced financial hardship, were affiliated with a church or religion, or scored low in Conscientiousness showed the most pronounced decrease in self-esteem during the years approaching marital dissolution.ConclusionThis study highlights the importance of assessing people multiple times before and after marital dissolution to dissect how people approach and respond to this life event. Results are consistent with perspectives that view divorce as an opportunity to abate the strains of an unhappy marriage

Histone Modifications within the Human X Centromere Region

Human centromeres are multi-megabase regions of highly ordered arrays of alpha satellite DNA that are separated from chromosome arms by unordered alpha satellite monomers and other repetitive elements. Complexities in assembling such large repetitive regions have limited detailed studies of centromeric chromatin organization. However, a genomic map of the human X centromere has provided new opportunities to explore genomic architecture of a complex locus. We used ChIP to examine the distribution of modified histones within centromere regions of multiple X chromosomes. Methylation of H3 at lysine 4 coincided with DXZ1 higher order alpha satellite, the site of CENP-A localization. Heterochromatic histone modifications were distributed across the 400–500 kb pericentromeric regions. The large arrays of alpha satellite and gamma satellite DNA were enriched for both euchromatic and heterochromatic modifications, implying that some pericentromeric repeats have multiple chromatin characteristics. Partial truncation of the X centromere resulted in reduction in the size of the CENP-A/Cenp-A domain and increased heterochromatic modifications in the flanking pericentromere. Although the deletion removed ∼1/3 of centromeric DNA, the ratio of CENP-A to alpha satellite array size was maintained in the same proportion, suggesting that a limited, but defined linear region of the centromeric DNA is necessary for kinetochore assembly. Our results indicate that the human X centromere contains multiple types of chromatin, is organized similarly to smaller eukaryotic centromeres, and responds to structural changes by expanding or contracting domains

Enterprise architecture driven design of an artefact to support strategic Information Technology decision-making of Small Enterprises in Nigeria and South Africa

Information Technology (IT) is inevitably influencing the way enterprises operate, compete, and grow. The contemporary disruption has not excluded small companies. Small enterprises play a significant role in the growth of every economy but are hindered by limited skills, time, and money. The attributes of small enterprises influence the strategic and day-to-day operations. Small enterprise owners are often the managers who make the strategic decisions in order to solve specific problems. The decision style of small enterprise owner-managers limits the leveraging of IT. To ensure the sustainability of small enterprises in a contemporary business ecosystem, it is pertinent to strategise IT investment decisions. Enterprise architecture is a well-known approach to business and IT alignment. This study aimsto discover and develop how the complex enterprise architecture principles can strategise the IT decisionmaking process in small enterprises with limited resources and informal structures. The pragmatic philosophic stance was the premise for understanding the decision challenges and the development of a roadmap to intervene the problems the researcher identified. The Vaishnavi and Kuechler design science research methodology guided this study. The qualitative research approach was employed to collect verbal data with eleven small enterprise ownermanagers to understand the processes and the challenges of making IT decision in small enterprises. A thematic analysis of the findings revealed that lack of formalisation, limited information, and lack of IT skill created a critical bottleneck of IT investment decisions in small enterprises. An enterprise architecture-driven framework was developed to overcome the bounded rationality approach to IT choices in small enterprises. The framework holistically assesses organisational business-IT capabilities, constraints, and criteria to guide the decisionmaker's choice. The characteristics of small enterprises limit the successful implementation of the enterprise architecture-driven framework as a theoretical guideline for making optimal IT decisions in small enterprises. This study further developed an online IT decision-assistive tool informed by the framework. The instantiation artefact was demonstrated with six small enterprise owners from Nigeria and South Africa. The findings affirmed the prospect, potential, and relevance of an enterprise architecture-driven artefact as a tool to optimise strategic IT decisions in small manufacturing, service, and retail enterprises. The artefact developed in this study provided a practical intervention to the challenges of IT investment decisions in small enterprises