A Systematic and Thorough Search for Domains of the Scavenger Receptor Cysteine-Rich Group-B Family in the Human Genome

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Bioinformatics tools for analysing viral genomic data

The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing

Spindle-E acts antivirally against alphaviruses in mosquito cells

Mosquitoes transmit several human- and animal-pathogenic alphaviruses (Togaviridae family). In alphavirus-infected mosquito cells two different types of virus-specific small RNAs are produced as part of the RNA interference response: short-interfering (si)RNAs and PIWI-interacting (pi)RNAs. The siRNA pathway is generally thought to be the main antiviral pathway. Although an antiviral activity has been suggested for the piRNA pathway its role in host defences is not clear. Knock down of key proteins of the piRNA pathway (Ago3 and Piwi5) in Aedes aegypti-derived cells reduced the production of alphavirus chikungunya virus (CHIKV)-specific piRNAs but had no effect on virus replication. In contrast, knock down of the siRNA pathway key protein Ago2 resulted in an increase in virus replication. Similar results were obtained when expression of Piwi4 was silenced. Knock down of the helicase Spindle-E (SpnE), an essential co-factor of the piRNA pathway in Drosophila melanogaster, resulted in increased virus replication indicating that SpnE acts as an antiviral against alphaviruses such as CHIKV and the related Semliki Forest virus (SFV). Surprisingly, this effect was found to be independent of the siRNA and piRNA pathways in Ae. aegypti cells and specific for alphaviruses. This suggests a small RNA-independent antiviral function for this protein in mosquitoes

Measurement and Enhancement of Cloud-based Online Gaming Systems

University of Minnesota M.S. thesis. July 2017. Major: Computer Science. Advisor: Haiyang Wang. 1 computer file (PDF); v, 54 pages.Cloud gaming refers to the technologies that offload parts of game software from traditional game consoles to powerful and elastic cloud infrastructure. This design effectively shifts the game system requirements as well as the necessary computational workload to remote cloud platforms and thus has been attracting an increasing amount of attention from both service providers and end users. We have seen commercial cloud gaming systems such as Gaikai and OnLive being available in the market with a considerable user base. However, the pitfalls as well as the design challenges of cloud gaming still remains largely unclear for the general public. In this thesis, we take an initial step towards the understanding of cloud gaming performance in virtualized environments. Different from existing cloud gaming implementations, we migrate the entire gaming system into a fully virtualized local cloud environment and compare its performance to a pure datacenter-based deployment. From our experiments, we find that the virtualized environment will significantly affect the latency as well as the frame rate of the game. As a result, we find the tested games running much slower on the cloud than on their non-virtualized counterpart. In particular, latency increases by about 176 ms and the frame rate decreases by almost 40% in our test platform. To make the matters worse, the resource utilization on the server also increases due to cloud virtualization. To address these issues, we propose a shared-memory-based enhancement to reduce the overhead of games running on virtualized environment. Our evaluation indicates that our approach can successfully reduce the cloud gaming latency by about 6% without noticeable increase of system's CPU and memory utilization

Culex quinquefasciatus mosquitoes do not support replication of Zika virus

The rapid spread of Zika virus (ZIKV) in the Americas raised many questions about the role of Culex quinquefasciatus mosquitoes in transmission, in addition to the key role played by the vector Aedes aegypti. Here we analysed the competence of Cx. quinquefasciatus (with or without Wolbachia endosymbionts) for a ZIKV isolate. We also examined the induction of RNA interference pathways after viral challenge and the production of small virus-derived RNAs. We did not observe any infection nor such small virus-derived RNAs, regardless of the presence or absence of Wolbachia. Thus, Cx. quinquefasciatus does not support ZIKV replication and Wolbachia is not involved in producing this phenotype. In short, these mosquitoes are very unlikely to play a role in transmission of ZIKV

Genome sequences of five African swine fever virus genotype IX isolates from domestic pigs in Uganda

Complete genome sequences of five African swine fever virus isolates were determined directly from clinical material obtained from domestic pigs in Uganda. Four sequences were essentially identical to each other, and all were closely related to the only known genome sequence of p72 genotype IX

Genome sequences of five African swine fever virus genotype IX isolates from domestic pigs in Uganda

Complete genome sequences of five African swine fever virus isolates were determined directly from clinical material obtained from domestic pigs in Uganda. Four sequences were essentially identical to each other, and all were closely related to the only known genome sequence of p72 genotype IX

Analysis of Paramyxovirus Transcription and Replication by High-Throughput Sequencing.

We have developed a high-throughput sequencing (HTS) workflow for investigating paramyxovirus transcription and replication. We show that sequencing of oligo(dT)-selected polyadenylated mRNAs, without considering the orientation of the RNAs from which they had been generated, cannot accurately be used to analyze the abundance of viral mRNAs because genomic RNA copurifies with the viral mRNAs. The best method is directional sequencing of infected cell RNA that has physically been depleted of ribosomal and mitochondrial RNA followed by bioinformatic steps to differentiate data originating from genomes from viral mRNAs and antigenomes. This approach has the advantage that the abundance of viral mRNA (and antigenomes) and genomes can be analyzed and quantified from the same data. We investigated the kinetics of viral transcription and replication during infection of A549 cells with parainfluenza virus type 2 (PIV2), PIV3, PIV5, or mumps virus and determined the abundances of individual viral mRNAs and readthrough mRNAs. We found that the mRNA abundance gradients differed significantly between all four viruses but that for each virus the pattern remained relatively stable throughout infection. We suggest that rapid degradation of non-poly(A) mRNAs may be primarily responsible for the shape of the mRNA abundance gradient in parainfluenza virus 3, whereas a combination of this factor and disengagement of RNA polymerase at intergenic sequences, particularly those at the NP:P and P:M gene boundaries, may be responsible in the other viruses.IMPORTANCE High-throughput sequencing (HTS) of virus-infected cells can be used to study in great detail the patterns of virus transcription and replication. For paramyxoviruses, and by analogy for all other negative-strand RNA viruses, we show that directional sequencing must be used to distinguish between genomic RNA and mRNA/antigenomic RNA because significant amounts of genomic RNA copurify with poly(A)-selected mRNA. We found that the best method is directional sequencing of total cell RNA, after the physical removal of rRNA (and mitochondrial RNA), because quantitative information on the abundance of both genomic RNA and mRNA/antigenomes can be simultaneously derived. Using this approach, we revealed new details of the kinetics of virus transcription and replication for parainfluenza virus (PIV) type 2, PIV3, PIV5, and mumps virus, as well as on the relative abundance of the individual viral mRNAs

HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression

Cytotoxic T lymphocyte (CTL) responses against the HIV Gag protein are associated with lowering viremia; however, immune control is undermined by viral escape mutations. The rapid viral mutation rate is a key factor, but recombination may also contribute. We hypothesized that CTL responses drive the outgrowth of unique intra-patient HIV-recombinants (URFs) and examined gag sequences from a Kenyan sex worker cohort. We determined whether patients with HLA variants associated with effective CTL responses (beneficial HLA variants) were more likely to carry URFs and, if so, examined whether they progressed more rapidly than patients with beneficial HLA-variants who did not carry URFs. Women with beneficial HLA-variants (12/52) were more likely to carry URFs than those without beneficial HLA variants (3/61) (p < 0.0055; odds ratio = 5.7). Beneficial HLA variants were primarily found in slow/standard progressors in the URF group, whereas they predominated in long-term non-progressors/survivors in the remaining cohort (p = 0.0377). The URFs may sometimes spread and become circulating recombinant forms (CRFs) of HIV and local CRF fragments were over-represented in the URF sequences (p < 0.0001). Collectively, our results suggest that CTL-responses associated with beneficial HLA variants likely drive the outgrowth of URFs that might reduce the positive effect of these CTL responses on disease progression

Epilepsia del lóbulo temporal: una revisión de tema sobre el abordaje diagnóstico

Introduction. According to the World Health Organization (WHO), epilepsy is one of the world’s most frequent neurological disorders. Epileptic seizures are considered to be a clinical manifestation caused by an excessive discharge of neurons in the brain. Its prevalence is higher in Latin America and the Caribbean than in developed countries. In most cases, seizures correspond to temporal lobe epilepsy, whose most common anatomic abnormality is hippocampal sclerosis. The objective is to present the basic epilepsy protocol in a standardized form and its usefulness in surgical planning, in order to perform a correct and timely diagnosis, knowing all of the tools that have been studied until now. Division of Covered Topics. A topic review of the existing literature in the Pubmed, Cochrane and Medline databases from 1980 to 2018 was performed on temporal lobe epilepsy. The anatomy, physiology, physiopathology, clinical presentation and imaging diagnosis of the pathology are concisely presented. Conclusions. This pathology is characterized by having an epileptogenic focus in the temporal lobes, with a high probability of control with surgical techniques that are becoming less aggressive. Diagnoses are made through clinics. However, new structural and functional imaging techniques are the diagnosis method of choice for patients suspected to have this pathology in order to make a more accurate and timely diagnosis.Introducción. Según la Organización Mundial de la Salud (OMS) la epilepsia constituye uno de los trastornos neurológicos más frecuentes en el mundo. Las crisis epilépticas se consideran una manifestación clínica originada por una descarga excesiva de neuronas a nivel cerebral. Su prevalencia es mayor en Latinoamérica y el Caribe que en países desarrollados; las crisis, en la mayoría de los casos, corresponden a la epilepsia del lóbulo temporal, cuya anormalidad anatómica más habitual es la esclerosis del hipocampo. El objetivo es exponer el protocolo básico de epilepsia de manera estandarizada y su utilidad en el planeamiento quirúrgico, y así, conociendo todas las herramientas estudiadas hasta el momento, se realice un adecuado y oportuno diagnóstico. División de los temas tratados. Se realizó una revisión de tema de la literatura existente en las bases de datos Pubmed, Cochrane y Medline desde 1980 hasta 2018 acerca de la epilepsia del lóbulo temporal. Se expone de manera concisa la anatomía, fisiología, fisiopatología, presentación clínica y diagnóstico imaginológico de la patología. Conclusiones. Esta patología se caracteriza por tener el foco epileptogénico en los lóbulos temporales con alta probabilidad de control con técnicas quirúrgicas cada vez menos agresivas. El diagnóstico es inducido a través de la clínica; sin embargo, las nuevas técnicas de imagen estructurales y funcionales son el método diagnóstico de elección en pacientes con sospecha de esta patología y, de esta manera, lograr la realización de un diagnóstico más certero y oportuno. [Araujo-Reyes AT, Sandoval J, Carrasco-Ore A, Baquero-Serrano MA. Epilepsia del lóbulo temporal: una revisión de tema sobre el abordaje diagnóstico. MedUNAB. 2019;22(2):228-241. doi:10.29375/01237047.3208