Environmental metagenomic samples and samples obtained as an attempt to identify a pathogen associated with the emergence of a novel infectious disease are important sources of novel microorganisms. The low costs and high throughput of sequencing technologies are expected to allow for the genetic material in those samples to be sequenced and the genomes of the novel microorganisms to be identified by alignment to those in a database of known genomes. Yet, for various biological and technical reasons, such alignment might not always be possible. We investigate a frequency analysis technique which on one hand allows for the identification of genetic material without relying on alignment and on the other hand makes possible the discovery of nonoverlapping contigs from the same organism. The technique is based on obtaining signatures of the genetic data and defining a distance/similarity measure between signatures. More precisely, the signatures of the genetic data are the frequencies of k-mers occurring in them, with k being a natural number. We considered an entropy-based distance between signatures, similar to the Kullback-Leibler distance in information theory, and investigated its ability to categorize negative-sense single-stranded RNA (ssRNA) viral genetic data. Our conclusion is that in this viral context, the technique provides a viable way of discovering genetic relationships without relying on alignment. We envision that our approach will be applicable to other microbial genetic contexts, e.g., other types of viruses, and will be an important tool in the discovery of novel microorganisms.
Trifonov, Vladimir; Rabadan, Raul
Cucumber mosaic virus (CMV) comprises numerous isolates with various levels of in-host diversity. Subgroup-distinctive features of the Fny and LS strains provided us with a platform to genetically map the viral control elements for genetic variation in planta. We found that both RNAs 1 and 2 controlled levels of genetic diversity, and further fine mapping revealed that the control elements of mutation frequency reside within the first 596 amino acids (aa) of RNA 1. The 2a/2b overlapping region of the 2a protein also contributed to control of viral genetic variation. Furthermore, the 3' nontranslated region (NTR) of RNA 3 constituted a hot spot of polymorphism, where the majority of fixed mutations found in the population were clustered. The 2b gene of CMV, a viral suppressor of gene silencing, controls the abundance of the fixed mutants in the viral population via a host-dependent mechanism. PMID:23115283
Pita, Justin S; Roossinck, Marilyn J
Classical methods for studying neuronal circuits are fairly low throughput. Transsynaptic viruses, particularly the pseudorabies (PRV) and rabies virus (RABV), and more recently vesicular stomatitis virus (VSV), for studying circuitry, is becoming increasingly popular. These higher throughput methods use viruses that transmit between neurons in either the anterograde or retrograde direction. Recently, a modified RABV for monosynaptic retrograde tracing was developed. (Figure 1A). In this method, the glycoprotein (G) gene is deleted from the viral genome, and resupplied only in targeted neurons. Infection specificity is achieved by substituting a chimeric G, composed of the extracellular domain of the ASLV-A glycoprotein and the cytoplasmic domain of the RABV-G (A/RG), for the normal RABV-G(1). This chimeric G specifically infects cells expressing the TVA receptor(1). The gene encoding TVA can been delivered by various methods(2-8). Following RABV-G infection of a TVA-expressing neuron, the RABV can transmit to other, synaptically connected neurons in a retrograde direction by nature of its own G which was co-delivered with the TVA receptor. This technique labels a relatively large number of inputs (5-10%)(2) onto a defined cell type, providing a sampling of all of the inputs onto a defined starter cell type. We recently modified this technique to use VSV as a transsynaptic tracer(9). VSV has several advantages, including the rapidity of gene expression. Here we detail a new viral tracing system using VSV useful for probing microcircuitry with increased resolution. While the original published strategies by Wickersham et al.(4) and Beier et al.(9) permit labeling of any neurons that project onto initially-infected TVA-expressing-cells, here VSV was engineered to transmit only to TVA-expressing cells (Figure 1B). The virus is first pseudotyped with RABV-G to permit infection of neurons downstream of TVA-expressing neurons. After infecting this first population of cells, the virus released can only infect TVA-expressing cells. Because the transsynaptic viral spread is limited to TVA-expressing cells, presence of absence of connectivity from defined cell types can be explored with high resolution. An experimental flow chart of these experiments is shown in Figure 2. Here we show a model circuit, that of direction-selectivity in the mouse retina. We examine the connectivity of starburst amacrine cells (SACs) to retinal ganglion cells (RGCs). PMID:23117695
Beier, Kevin; Cepko, Constance
Thirteen BVDV isolates collected in four geographic regions of India between 2000 and 2002 were typed in 5'-UTR. To confirm results of genetic typing, selected viruses were also analysed in the N(pro) region. Phylogenetic analysis revealed that all Indian BVDV isolates belong to BVDV-1b (Osloss-like group). Despite a long distance between the farms from which the viruses were isolated there was no correlation between the origin of viral isolates and their position in a phylogenetic tree. Higher genetic similarity of Indian BVDV isolates was observed most probably due to the uncontrolled movement of cattle as well as the uncontrolled use of semen from bulls for breeding of local and farm cattle in different states of India. PMID:15564029
Mishra, N; Pattnaik, B; Vilcek, S; Patil, S S; Jain, P; Swamy, N; Bhatia, S; Pradhan, H K
Purpose of Review Inflammatory bowel disease (IBD) is thought to occur in genetically susceptible individuals. However, environmental factors, potentially including shifts in commensal microbiota, are also required to trigger disease. This review discusses some of the recent discoveries in host susceptibility and interaction with the microbial environment, and pinpoints key areas for advancement in our understanding of IBD pathogenesis. Recent findings Meta-analyses of genome wide association studies have uncovered many new exciting genes associated with susceptibility loci. In addition, improved methods to analyze the commensal microbiota path the way to better define dysbiosis and its potential role in disease. Lastly, identification of viral triggers in experimental systems of IBD suggests a potential role in IBD. Summary Understanding the precise microbial and immune triggers of IBD in a genetic context will hopefully lead to a better understanding of the pathogenesis of this disease and the discovery of novel therapeutic approaches including vaccines for specific viruses.
Sun, Lulu; Nava, Gerardo M.; Stappenbeck, Thaddeus S.
Little is known about the factors that drive the high levels of between-host variation in pathogen burden that are frequently observed in viral infections. Here, two factors thought to impact viral load variability, host genetic diversity and stochastic processes linked with viral entry into the host, were examined. This work was conducted with the aquatic vertebrate virus, Infectious hematopoietic necrosis virus (IHNV), in its natural host, rainbow trout. It was found that in controlled in vivo infections of IHNV, a suggestive trend of reduced between-fish viral load variation was observed in a clonal population of isogenic trout compared to a genetically diverse population of out-bred trout. However, this trend was not statistically significant for any of the four viral genotypes examined, and high levels of fish-to-fish variation persisted even in the isogenic trout population. A decrease in fish-to-fish viral load variation was also observed in virus injection challenges that bypassed the host entry step, compared to fish exposed to the virus through the natural water-borne immersion route of infection. This trend was significant for three of the four virus genotypes examined and suggests host entry may play a role in viral load variability. However, high levels of viral load variation also remained in the injection challenges. Together, these results indicate that although host genetic diversity and viral entry may play some role in between-fish viral load variation, they are not major factors. Other biological and non-biological parameters that may influence viral load variation are discussed.
Wargo, Andrew R.; Kell, Alison M.; Scott, Robert J.; Thorgaard, Gary H.; Kurath, Gael
The present invention provides materials and methods for researching poultry viruses, particularly for researching infectious bronchitis viruses in poultry. Also provided are materials and methods useful for reducing the economic impact that infectious bronchitis disease has on poultry production. In one aspect of the invention, there are provided nucleic acids, amino acids and related materials and compositions useful for combating infectious bronchitis virus in poultry.
Dengue is the most widespread mosquito-borne human viral disease. The disease is now endemic in more than 100 countries in Africa, the Americas, the Eastern Mediterranean, South-East Asia and the Western Pacific regions. Dengue viruses cause dengue infection, which ranges from mild febrile illness (dengue fever, DF) to fatal haemorrhagic manifestation (dengue haemorrhagic fever, DHF) leading to shock syndrome (dengue
Suchita Chaudhry; Sathyamangalam Swaminathan; Navin Khanna
riophages in connection with the study of viruses and cell biology; and (e) unknown aspects of lysogeny and When people spoke of microbes in the early 1900s, colicinogeny described long ago and possibly connected they were thinking almost exclusively of bacterial (and with new findings on imprinting in bacteria. viral) pathogens affecting humans. Of course, Antonie Microbiology has undeniably played
James F. Crow; William F. Dove; Jean-Pierre Gratia
Viral hemorrhagic septicemia virus (VHSV) is a fish rhabdovirus that causes disease in a broad range of marine and freshwater hosts. The known geographic range includes the Northern Atlantic and Pacific Oceans, and recently it has invaded the Great Lakes region of North America. The goal of this work was to characterize genetic diversity of Great Lakes VHSV isolates at the early stage of this viral emergence by comparing a partial glycoprotein (G) gene sequence (669 nt) of 108 isolates collected from 2003 to 2009 from 31 species and at 37 sites. Phylogenetic analysis showed that all isolates fell into sub-lineage IVb within the major VHSV genetic group IV. Among these 108 isolates, genetic diversity was low, with a maximum of 1.05% within the 669 nt region. There were 11 unique sequences, designated vcG001 to vcG011. Two dominant sequence types, vcG001 and vcG002, accounted for 90% (97 of 108) of the isolates. The vcG001 isolates were most widespread. We saw no apparent association of sequence type with host or year of isolation, but we did note a spatial pattern, in which vcG002 isolates were more prevalent in the easternmost sub-regions, including inland New York state and the St. Lawrence Seaway. Different sequence types were found among isolates from single disease outbreaks, and mixtures of types were evident within 2 isolates from individual fish. Overall, the genetic diversity of VHSV in the Great Lakes region was found to be extremely low, consistent with an introduction of a new virus into a geographic region with previously naïve host populations.
Thompson, T. M.; Batts, W. N.; Faisal, M.; Bowser, P.; Casey, J. W.; Phillips, K.; Garver, K. A.; Winton, J.; Kurath, G.
The distribution and intensity of transmission of vector-borne pathogens can be strongly influenced by the competence of vectors. Vector competence, in turn, can be influenced by temperature and viral genetics. West Nile virus (WNV) was introduced into the United States of America in 1999 and subsequently spread throughout much of the Americas. Previously, we have shown that a novel genotype
A. Marm Kilpatrick; Mark A. Meola; Robin M. Moudy; Laura D. Kramer
Infecting rhesus macaques (Macaca mulatta) with the simian immunodeficiency virus (SIV) is an established animal model of human immunodeficiency virus (HIV) pathogenesis. Many studies have used various derivatives of the SIVmac251 viral swarm to investigate several aspects of the disease, including transmission, progression, response to vaccination, and SIV/HIV-associated neurological disorders. However, the lack of standardization of the infecting inoculum complicates comparative analyses. We investigated the genetic diversity and phylogenetic relationships of the 1991 animal-titered SIVmac251 swarm, the peripheral blood mononuclear cell (PBMC) passaged SIVmac251, and additional SIVmac251 sequences derived over the past 20 years. Significant sequence divergence and diversity were evident among the different viral sources. This finding highlights the importance of characterizing the exact source and genetic makeup of the infecting inoculum to achieve controlled experimental conditions and enable meaningful comparisons across studies. PMID:21524235
Strickland, Samantha L; Gray, Rebecca R; Lamers, Susanna L; Burdo, Tricia H; Huenink, Ellen; Nolan, David J; Nowlin, Brian; Alvarez, Xavier; Midkiff, Cecily C; Goodenow, Maureen M; Williams, Kenneth; Salemi, Marco
Abstract Infecting rhesus macaques (Macaca mulatta) with the simian immunodeficiency virus (SIV) is an established animal model of human immunodeficiency virus (HIV) pathogenesis. Many studies have used various derivatives of the SIVmac251 viral swarm to investigate several aspects of the disease, including transmission, progression, response to vaccination, and SIV/HIV-associated neurological disorders. However, the lack of standardization of the infecting inoculum complicates comparative analyses. We investigated the genetic diversity and phylogenetic relationships of the 1991 animal-titered SIVmac251 swarm, the peripheral blood mononuclear cell (PBMC) passaged SIVmac251, and additional SIVmac251 sequences derived over the past 20 years. Significant sequence divergence and diversity were evident among the different viral sources. This finding highlights the importance of characterizing the exact source and genetic makeup of the infecting inoculum to achieve controlled experimental conditions and enable meaningful comparisons across studies.
Strickland, Samantha L.; Gray, Rebecca R.; Lamers, Susanna L.; Burdo, Tricia H.; Huenink, Ellen; Nolan, David J.; Nowlin, Brian; Alvarez, Xavier; Midkiff, Cecily C.; Goodenow, Maureen M.; Williams, Kenneth
Basic research has been conducted on genetic engineering and synthesis of light-activated protein bacteriorhodopsin, and on a number of analogs for use in device application based on development of new photonic materials derived from bacteriorhodopsin.
Venezuelan equine encephalitis (VEE) is a reemerging, mosquito-borne viral disease of the neotropics that is severely debilitating and sometimes fatal to humans. Periodic epidemics mediated by equine amplification have been recognized since the 1920s, but interepidemic disease is rarely recognized. We report here clinical findings and genetic characterization of 42 cases of endemic VEE detected in Panama from 1961–2004. Recent
Evelia Quiroz; Patricia V. Aguilar; Julio Cisneros; Robert B. Tesh; Scott C. Weaver
OBJECTIVE:Hepatitis C virus (HCV) is known to be heterogeneous and to circulate as a group of closely related quasispecies in individual patients, although hepatic viral genetic characteristics have not been well documented.METHODS:Matched serum and liver samples were tested by reverse transcription polymerase chain reaction amplification and single stranded conformation polymorphism analysis of the hypervariable portion of the E2\\/NS1 region of
Xiaofeng Fan; Harvey Solomon; John E Poulos; Brent A Neuschwander-Tetri; Adrian M Di Bisceglie
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation. Transmission dynamics can be considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Patterns of viral genetic variation will also be affected by selection acting on viral phenotypes. Although viruses can differ with respect to many phenotypes, phylodynamic studies have to date tended to focus on a limited number of viral phenotypes. These include virulence phenotypes, phenotypes associated with viral transmissibility, cell or tissue tropism phenotypes, and antigenic phenotypes that can facilitate escape from host immunity. Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread , spatio-temporal dynamics including metapopulation dynamics , zoonotic transmission, tissue tropism , and antigenic drift . The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics.
Volz, Erik M.; Koelle, Katia; Bedford, Trevor
The Nature of Genetic Material, a new resource from Baylor College of MedicineÃ¢ÂÂs comprehensive website, BioEd Online, is one module of a three-part, interactive Web-based course called Genes, Health and Society. [The course, which explores the rapidly evolving world of genetics and genomics, can be taken free of charge for professional or personal development. Each module stands alone. Educators can work through the modules in sequence or move freely among them.
Center for Educational Outreach and Center for Collaborative and Interactive Technologies * (Baylor College of Medicine;)
Specific human polymorphisms, most commonly found in Central Africa, can predict the success of drug treatment against the hepatitis C virus (HCV), a significant and globally-distributed human pathogen. However, this association is only found for a subset of HCV genotypes. Despite receiving considerable attention in the medical and virological literature, no evolutionary explanation for this curious pattern has been put forward. Here we suggest that the 'drug treatment resistance' phenotype exhibited today by some HCV genotypes evolved hundreds to thousands of years ago in response to human genetic variation local to Central Africa: an adaptation that has since accrued a new function in the era of anti-viral drug treatment. This could represent one of the oldest known examples of viral exaptation at the population level. PMID:24140473
Rose, Rebecca; Markov, Peter V; Lam, Tommy T; Pybus, Oliver G
Human disease caused by highly pathogenic avian influenza (H5N1) is associated with fulminant viral pneumonia and mortality rates in excess of 60%. Cytokine dysregulation is thought to contribute to its pathogenesis. In comparison with human seasonal influenza (H1N1) viruses, clade 1, 2.1, and 2.2 H5N1 viruses induced higher levels of tumor necrosis factor-? in primary human macrophages. To understand viral genetic determinants responsible for this hyperinduction of cytokines, we constructed recombinant viruses containing different combinations of genes from high-cytokine (A/Vietnam/1203/04) and low-cytokine (A/WSN/33) phenotype H1N1 viruses and tested their cytokine-inducing phenotype in human macrophages. Our results suggest that the H5N1 polymerase gene segments, and to a lesser extent the NS gene segment, contribute to cytokine hyperinduction in human macrophages and that a putative H5 pandemic virus that may arise through genetic reassortment between H5N1 and one of the current seasonal influenza viruses may have a markedly altered cytokine phenotype.
Cheung, Chung Y.; Chan, Michael C.; Lee, Suki M. Y.; Nicholls, John M.; Guan, Yi; Peiris, Joseph S. M.
Summary Genetic modification of dendritic cells (DCs) with recombinant vectors encoding tumor antigens may aid in developing new immunotherapeutic treatments for patients with cancer. Here, we characterized antigen presentation by human DCs genetically modified with plasmid cDNAs, RNAs, adenoviruses, or retroviruses, encoding the melanoma antigen gp100 or the tumor-testis antigen NY-ESO-1. Monocyte-derived DCs were electroporated with cDNAs or RNAs, or transduced with adenoviruses. CD34+ hematopoietic stem cell-derived DCs were used for retroviral transduction. Genetically modified DCs were coincubated with CD8+ and CD4+ T cells that recognized major histocompatibility complex class I- and class II-restricted epitopes from gp100 and NY-ESO-1, and specific recognition was evaluated by interferon? secretion. Cytokine release by both CD8+ and CD4+ T cells was consistently higher in response to DCs modified with adenoviruses than cDNAs or RNAs, and maturation of DCs after genetic modification did not consistently alter patterns of recognition. Also, retrovirally transduced DCs encoding gp100 were well recognized by both CD8+ and CD4+ T cells. These data suggest that DCs transduced with viral vectors may be more efficient than DCs transfected with cDNAs or RNAs for the induction of tumor reactive CD8+ and CD4+ T cells in vitro and in human vaccination trials.
Lotem, Michal; Zhao, Yangbing; Riley, John; Hwu, Patrick; Morgan, Richard A.; Rosenberg, Steven A.; Parkhurst, Maria R.
Bovine viral diarrhoea virus (BVDV) is an important cattle pathogen that causes acute or persistent infections. These are associated with immunotolerance to the viral strain persisting in animals that became infected early in their intrauterine development. To this date, the epidemiology of BVD in Switzerland runs virtually undisturbed by control measures such as restrictions on animal traffic or vaccination. Here, we analysed the viral genetics of 169 Swiss isolates and carried out crossed serum neutralisation tests to assess the antigenic spectrum of BVDV strains present in the cattle population. Besides confirming the presence of BVDV type 1 subgroups b, e, h and k, a single "orphan" BVDV-1 virus was detected that does not belong to any known BVDV-1 subgroup. No BVDV type 2 viruses were detected, suggesting that they are rare or not present in the cattle population. Antigenic comparison revealed significant differences between the different subgroups, with anti-1k immune serum having up to tenfold lower neutralising activity against 1b, 1e and 1h subgroup viruses, which however may still suffice to protect 1k-immune animals against superinfection by viruses of those other subgroups. Serum from routinely vaccinated animals revealed generally low titres but good cross-neutralisation. A geographic information system revealed that the viruses of the different subgroups are distributed in an apparently randomised fashion in the cattle population. This geographic distribution pattern may reflect peculiarities of the management practice in the Swiss cattle industry that, especially through annual transhumance of up to 25% of the entire population in the alpine region, tend to optimise the spread of BVDV. PMID:18424020
Bachofen, Claudia; Stalder, Hanspeter; Braun, Ueli; Hilbe, Monika; Ehrensperger, Felix; Peterhans, Ernst
Tomato spotted wilt virus (TSWV) is transmitted exclusively by thrips in nature. A reassortment-based viral genetic system was used to map transmissibility by thrips to the medium (M) RNA of TSWV. To locate determinants of thrips transmission in the M RNA, 30 single-lesion isolates (SLIs) were generated from a single TSWV isolate that was inefficiently transmitted by thrips. Three of the 30 SLIs were transmitted by thrips, and 27 were not. Sequence analysis of the M RNA, thrips transmissibility assays, GC protein analysis, and transmission electron microscopic studies revealed that a specific nonsynonymous mutation (C1375A) in the GN/GC ORF of the M RNA resulted in the loss of thrips transmissibility without inhibition of virion assembly. This was in contrast to other nontransmissible SLIs, which had frameshift and/or nonsense mutations in the GN/GC ORF but were defective in virion assembly. The GC glycoprotein was detectable in the C1375A mutants but not in the frameshift or nonsense mutants. We report a specific viral determinant associated with virus transmission by thrips. In addition, the loss of transmissibility was associated with the accumulation of defective haplotypes in the population, which are not transmissible by thrips, rather than with the presence of a dominant haplotype that is inefficiently transmitted by thrips. These results also indicate that the glycoproteins may not be required for TSWV infection of plant hosts but are required for transmissibility by thrips.
Sin, Sang-Hoon; McNulty, Brian C.; Kennedy, George G.; Moyer, James W.
Neonatal intraventricular injection of adeno-associated virus has been shown to transduce neurons widely throughout the brain, but its full potential for experimental neuroscience has not been adequately explored. We report a detailed analysis of the method’s versatility with an emphasis on experimental applications where tools for genetic manipulation are currently lacking. Viral injection into the neonatal mouse brain is fast, easy, and accesses regions of the brain including cerebellum and brain stem that have been difficult to target with other techniques such as electroporation. We show that viral transduction produces an inherently mosaic expression pattern that can be exploited by varying the titer to transduce isolated neurons or densely-packed populations. We demonstrate that expression of virally-encoded proteins is active much sooner than previously believed, allowing genetic perturbation during critical periods of neuronal plasticity, but is also long-lasting and stable, allowing chronic studies of aging. We harness these features to visualize and manipulate neurons in the hindbrain that have been recalcitrant to approaches commonly applied in the cortex. We show that viral labeling aids the analysis of postnatal dendritic maturation in cerebellar Purkinje neurons by allowing individual cells to be readily distinguished, and then demonstrate that the same sparse labeling allows live in vivo imaging of mature Purkinje neurons at resolution sufficient for complete analytical reconstruction. Given the rising availability of viral constructs, packaging services, and genetically modified animals, these techniques should facilitate a wide range of experiments into brain development, function, and degeneration.
Kim, Ji-Yoen; Ash, Ryan T.; Ceballos-Diaz, Carolina; Levites, Yona; Golde, Todd E.; Smirnakis, Stelios M.; Jankowsky, Joanna L.
The maintenance of female polyandry has traditionally been attributed to the material (direct) benefits derived from male mating resources (e.g. nuptial gifts) accrued by multiple mating. However, genetic (indirect) benefits offer a more robust explanation since only polyandrous, not monandrous, females may gain both material benefits from multiple mating and genetic benefits from multiple sires. Discriminating between material and genetic
Kenneth M. Fedorka; Timothy A. Mousseau
Genetic materials are one of the most important and fundamental research resources for studying biological phenomena. Scientific need for genetic materials has been increasing and will never cease. Ever since it was established as RIKEN DNA Bank in 1987, the Gene Engineering Division of RIKEN BioResource Center (BRC) has been engaged in the collection, maintenance, storage, propagation, quality control, and distribution of genetic resources developed mainly by the Japanese research community. When RIKEN BRC was inaugurated in 2001, RIKEN DNA Bank was incorporated as one of its six Divisions, the Gene Engineering Division. The Gene Engineering Division was selected as a core facility for the genetic resources of mammalian and microbe origin by the National BioResource Project (NBRP) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan in 2002. With support from the scientific community, the Division now holds over 3 million clones of genetic materials for distribution. The genetic resources include cloned DNAs, gene libraries (e.g., cDNA and genomic DNA cloned into phage, cosmid, BAC, phosmid, and YAC), vectors, hosts, recombinant viruses, and ordered library sets derived from animal cells, including human and mouse cells, microorganisms, and viruses. Recently genetic materials produced by a few MEXT national research projects were transferred to the Gene Engineering Division for further dissemination. The Gene Engineering Division performs rigorous quality control of reproducibility, restriction enzyme mapping and nucleotide sequences of clones to ensure the reproducibility of in vivo and in vitro experiments. Users can easily access our genetic materials through the internet and obtain the DNA resources for a minimal fee. Not only the materials, but also information of features and technology related to the materials are provided via the web site of RIKEN BRC. Training courses are also given to transfer the technology for handling viral vectors. RIKEN BRC supports scientists around the world in the use of valuable genetic materials. PMID:20484845
Yokoyama, Kazunari K; Murata, Takehide; Pan, Jianzhi; Nakade, Koji; Kishikawa, Shotaro; Ugai, Hideyo; Kimura, Makoto; Kujime, Yukari; Hirose, Megumi; Masuzaki, Satoko; Yamasaki, Takahito; Kurihara, Chitose; Okubo, Masato; Nakano, Yuri; Kusa, Yuka; Yoshikawa, Akiko; Inabe, Kumiko; Ueno, Kazuko; Obata, Yuichi
This article outlines a research program for an anthropology of viral hemorrhagic fevers (collectively known as VHFs). It begins by reviewing the social science literature on Ebola, Marburg, and Lassa fevers and charting areas for future ethnographic attention. We theoretically elaborate the hotspot as a way of integrating analysis of the two routes of VHF infection: from animal reservoirs to humans and between humans. Drawing together recent anthropological investigations of human-animal entanglements with an ethnographic interest in the social production of space, we seek to enrich conceptualizations of viral movement by elaborating the circumstances through which viruses, humans, objects, and animals come into contact. We suggest that attention to the material proximities-between animals, humans, and objects-that constitute the hotspot opens a frontier site for critical and methodological development in medical anthropology and for future collaborations in VHF management and control. PMID:24752909
Brown, Hannah; Kelly, Ann H
Viral infection of mammalian cells entails the regulated induction of viral gene expression. The induction of many viral genes, including the herpes simplex virus gene encoding thymidine kinase (tk), depends on viral regulatory proteins that act in trans. Because recognition of the tk promoter by cellular transcription factors is well understood, its trans induction by viral regulatory proteins may serve as a useful model for the regulation of eukaryotic gene expression. A comprehensive set of mutations was therefore introduced into the chromosome of herpes simplex virus at the tk promoter to directly analyze the effects of promoter mutations on tk transcription. The promoter domains required for efficient tk expression under conditions of trans induction corresponded to those important for recognition by cellular transcription factors. Thus, trans induction of tk expression may be catalyzed initially by the interaction of viral regulatory proteins with cellular transcription factors.
Coen, Donald M.; Weinheimer, Steven P.; McKnight, Steven L.
The aims of this study were to estimate genetic (co)variance components of Atlantic cod for body weight at 2.5years of age (BW) and resistance to vibriosis (a bacterial disease) and viral nervous necrosis (VNN). The traits were recorded on seven discrete year-classes: five year-classes for vibriosis (11,936 individuals), two year-classes for VNN (6185 individuals) and five year-classes for BW (22,703
Rama Bangera; Jørgen Ødegård; Anne Kettunen Præbel; Atle Mortensen; Hanne Marie Nielsen
Bovine viral diarrhoea (BVD) is an economically important cattle disease with a world-wide distribution that is caused by BVD virus, a pestivirus of the flaviviridae family. BVD viruses are genetically highly variable. They are classified into two genetic species (BVDV-1 and -2) that are further divided into numerous subgroups, particularly for BVDV-1. The complexity of these viruses is also reflected in their interaction with the host animals. Infections are either transient or persistent and can cause a wide spectrum of clinical signs, from no or very mild disease to severe forms, reminiscent of viral haemorrhagic fevers. In this work, we have analysed the clinical signs and the pathology of BVD viral infections in a cattle population where different subgroups of BVDV-1 genotype viruses are endemic. In addition, we have examined potential virulence properties of BVDV-1 subgroups during persistent infection by comparing the viral subgroups present in clinical cases with those detected in persistently infected (PI) animals sampled for epidemiological criteria, irrespective of their health condition. Furthermore, the clinical and postmortem findings were compared with respect to genetic characteristics of the viruses isolated from these animals. Our results indicate that the BVDV positive animals fall roughly into two categories, depending on the primary organ affected and the age, with lung-centred pathology occurring mainly in young animals and mucosal pathology predominantly in older animals. Furthermore, we found a markedly higher proportion of representatives of the BVDV-1e subgroup in stillborn calves and aborted foetuses originating from epidemically unrelated cattle herds, suggesting that BVDV-1e may play a special role in prenatal and perinatal losses. PMID:19819088
Bachofen, Claudia; Braun, Ueli; Hilbe, Monika; Ehrensperger, Felix; Stalder, Hanspeter; Peterhans, Ernst
This catalogue, prepared by the National Clearinghouse for Human Genetic Diseases, provides educational and informational materials on the latest advances in testing, diagnosing, counseling, and treating individuals with a concern for genetic diseases. The materials include books, brochures, pamphlets, journal articles, audio cassettes,…
National Clearinghouse for Human Genetic Diseases (DHEW/PHS), Rockville, MD.
Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients. PMID:24722365
Qi, Hangfei; Olson, C Anders; Wu, Nicholas C; Ke, Ruian; Loverdo, Claude; Chu, Virginia; Truong, Shawna; Remenyi, Roland; Chen, Zugen; Du, Yushen; Su, Sheng-Yao; Al-Mawsawi, Laith Q; Wu, Ting-Ting; Chen, Shu-Hua; Lin, Chung-Yen; Zhong, Weidong; Lloyd-Smith, James O; Sun, Ren
Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be to reinterpreted in light of viral knowledge or we need to develop new theory from the viral point-of-view. Here we briefly introduce our viral planet and then address a major outstanding question in biology: why is most of life viral? A key insight is that during an infection cycle the original virus is completely broken down and only the associated information is passed on to the next generation. This is different for cellular organisms, which must pass on some physical part of themselves from generation to generation. Based on this premise, it is proposed that the thermodynamic consequences of physical information (e.g., Landauer's principle) are observed in natural viral populations. This link between physical and genetic information is then used to develop the Viral Information Hypothesis, which states that genetic information replicates itself to the detriment of system energy efficiency (i.e., is viral in nature). Finally, we show how viral information can be tested, and illustrate how this novel view can explain existing ecological and evolutionary theories from more fundamental principles. PMID:23482918
Rohwer, Forest; Barott, Katie
Based on personal acquaintances and experience dating back to the early 1950s, the senior author reviews the history of viral\\u000a therapy of cancer. He points out the difficulties encountered in the treatment of human cancers, as opposed by the highly\\u000a successful viral therapy of experimentally maintained tumors in laboratory animals, especially that of ascites carcinomas\\u000a in mice. A detailed account
Joseph G. Sinkovics; Joseph C. Horvath
The herpes simplex virus 1 (HSV-1) UL3 protein is a nuclear phosphoprotein of unknown function. Previous studies have shown that UL3 phosphorylation is mediated by the HSV-1 viral kinase UL13, and that UL3 colocalizes with other viral nuclear proteins (Jahedi et al 1999; Markovitz et al 1999; Markovitz and Roizman 2000; Ward et al 2000).While exploring functional interactions of UL3,
Megan J. Dambach; Jordan Trecki; Natalia Martin; Nancy S. Markovitz
Genetic recombination in RNA viruses was discovered many years ago for poliovirus (PV), an enterovirus of the Picornaviridae family, and studied using PV or other picornaviruses as models. Recently, recombination was shown to be a general phenomenon between different types of enteroviruses of the same species. In particular, the interest for this mechanism of genetic plasticity was renewed with the emergence of pathogenic recombinant circulating vaccine-derived polioviruses (cVDPVs), which were implicated in poliomyelitis outbreaks in several regions of the world with insufficient vaccination coverage. Most of these cVDPVs had mosaic genomes constituted of mutated poliovaccine capsid sequences and part or all of the non-structural sequences from other human enteroviruses of species C (HEV-C), in particular coxsackie A viruses. A study in Madagascar showed that recombinant cVDPVs had been co-circulating in a small population of children with many different HEV-C types. This viral ecosystem showed a surprising and extensive biodiversity associated to several types and recombinant genotypes, indicating that intertypic genetic recombination was not only a mechanism of evolution for HEV-C, but an usual mode of genetic plasticity shaping viral diversity. Results suggested that recombination may be, in conjunction with mutations, implicated in the phenotypic diversity of enterovirus strains and in the emergence of new pathogenic strains. Nevertheless, little is known about the rules and mechanisms which govern genetic exchanges between HEV-C types, as well as about the importance of intertypic recombination in generating phenotypic variation. This review summarizes our current knowledge of the mechanisms of evolution of PV, in particular recombination events leading to the emergence of recombinant cVDPVs.
Combelas, Nicolas; Holmblat, Barbara; Joffret, Marie-Line; Colbere-Garapin, Florence; Delpeyroux, Francis
Paramyxoviral infections cause most of the acute lower respiratory tract illness in infants and young children and predispose to the development of chronic wheezing, but the relationship between these short- and long-term viral effects are uncertain. Here we show that a single paramyxoviral infection of mice (C57BL6/J strain) not only produces acute bronchiolitis, but also triggers a chronic response with airway hyperreactivity and goblet cell hyperplasia lasting at least a year after complete viral clearance. During the acute response to virus, same-strain ICAM-1–null mice are protected from airway inflammation and hyperreactivity despite similar viral infection rates, but the chronic response proceeds despite ICAM-1 deficiency. Neither response is influenced by IFN-? deficiency, but the chronic response is at least partially prevented by glucocorticoid treatment. In contrast to viral infection, allergen challenge caused only short-term expression of asthma phenotypes. Thus, paramyxoviruses cause both acute airway inflammation/hyperreactivity and chronic airway remodeling/hyperreactivity phenotypes (the latter by a hit-and-run strategy, since viral effects persist after clearance). These two phenotypes can be segregated by their dependence on the ICAM-1 gene and so depend on distinct controls that appear critical for the development of lifelong airway diseases such as asthma.
Walter, Michael J.; Morton, Jeffrey D.; Kajiwara, Naohiro; Agapov, Eugene; Holtzman, Michael J.
The purpose of this project was to provide innovative and cutting edge genetics materials for 14-17 year olds (Year 10-12) in Australian schools, which aimed to engage students and encourage evidence based decision-making. In 2008, an Australian School Innovation in Science, Technology and Mathematics (ASISTM) project called "Genetics Education in…
Dawson, Vaille; Carson, Katherine; Venville, Grady
Most of the activities suggested in this trial version of the Genetics unit produced by the Australian Science Education Project rely on second-hand data, although one of the introductory activities suggested is based on results of a mouse breeding experiment. The unit is, therefore, expected to be suitable only for students who are capable of…
Australian Science Education Project, Toorak, Victoria.
The rat parvovirus H-1PV is a promising anticancer agent given its oncosuppressive properties and the absence of known side effects in humans. H-1PV replicates preferentially in transformed cells, but the virus can enter both normal and cancer cells. Uptake by normal cells sequesters a significant portion of the administered viral dose away from the tumor target. Hence, targeting H-1PV entry specifically to tumor cells is important to increase the efficacy of parvovirus-based treatments. In this study, we first found that sialic acid plays a key role in H-1PV entry. We then genetically engineered the H-1PV capsid to improve its affinity for human tumor cells. By analogy with the resolved crystal structure of the closely related parvovirus minute virus of mice, we developed an in silico three-dimensional (3D) model of the H-1PV wild-type capsid. Based on this model, we identified putative amino acids involved in cell membrane recognition and virus entry at the level of the 2-fold axis of symmetry of the capsid, within the so-called dimple region. In situ mutagenesis of these residues significantly reduced the binding and entry of H-1PV into permissive cells. We then engineered an entry-deficient viral capsid and inserted a cyclic RGD-4C peptide at the level of its 3-fold axis spike. This peptide binds ?v?3 and ?v?5 integrins, which are overexpressed in cancer cells and growing blood vessels. The insertion of the peptide rescued viral infectivity toward cells overexpressing ?v?5 integrins, resulting in the efficient killing of these cells by the reengineered virus. This work demonstrates that H-1PV can be genetically retargeted through the modification of its capsid, showing great promise for a more efficient use of this virus in cancer therapy.
Allaume, Xavier; El-Andaloussi, Nazim; Leuchs, Barbara; Bonifati, Serena; Kulkarni, Amit; Marttila, Tiina; Kaufmann, Johanna K.; Nettelbeck, Dirk M.; Kleinschmidt, Jurgen; Rommelaere, Jean
DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material. PMID:23281109
Pinheiro, Vitor B; Loakes, David; Holliger, Philipp
Poliovirus RNA-dependent RNA polymerase 3D and viral protein 3AB are both thought to be required for the initiation of RNA synthesis. These two proteins physically associate with each other and with viral RNA replication complexes found on virus-induced membranes in infected cells. An understanding of the interface between 3D and 3AB would provide a first step in visualizing the architecture of the multiprotein complex that is assembled during poliovirus infection to replicate and package the viral RNA genome. The identification of mutations in 3D that diminish 3D-3AB interactions without affecting other functions of 3D polymerase is needed to study the function of the 3D-3AB interaction in infected cells. We describe the use of the yeast two-hybrid system to isolate and characterize mutations in 3D polymerase that cause it to interact less efficiently with 3AB than wild-type polymerase. One mutation, a substitution of leucine for valine at position 391 (V391L), resulted in a 3AB-specific interaction defect in the two-hybrid system, causing a reduction in the interaction of 3D polymerase with 3AB but not with another viral protein or a host protein tested. In vitro, purified 3D-V391L polymerase bound to membrane-associated 3AB with reduced affinity. Poliovirus that contained the 3D-V391L mutation was temperature sensitive, displaying a pronounced conditional defect in RNA synthesis. We conclude that interaction between 3AB and 3D or 3D-containing polypeptides plays a role in RNA synthesis during poliovirus infection.
Hope, D A; Diamond, S E; Kirkegaard, K
Novel suppressor variants of conditionally lethal HSV-1 gamma34.5 deletion mutants have been isolated which exhibit restored ability to grow on neoplastic neuronal cells. Deletion of the viral gamma34.5 genes, whose products share functional similarity with the cellular GADD34 gene, renders the virus non-neurovirulent and imposes a block to viral replication in neuronal cells. Protein synthesis ceases at late times post-infection and the translation initiation factor eIF2alpha is phosphorylated by the cellular PKR kinase [Chou et al. (1990) Science, 252, 1262-1266; (1995) Proc. Natl Acad. Sci. USA, 92, 10516-10520]. The suppressor mutants have overcome the translational block imposed by PKR. Multiple, independent isolates all contain rearrangements within a 595 bp element in the HSV-1 genome where the unique short component joins the terminal repeats. This alteration, which affects the production of the viral mRNA and protein from the Us11 and Us12 genes, is both necessary and sufficient to confer the suppressor phenotype on gamma34.5 mutant viruses. HSV-1 thus encodes a specific element which inhibits ongoing protein synthesis in the absence of the viral GADD34-like function. Since this inhibition involves the accumulation of phosphorylated eIF2alpha, the element identified by the suppressor mutations may be a discrete PKR activator. Activation of the PKR kinase thus does not proceed through a general, cellular 'antiviral' sensing mechanism. Instead, the virus deliberately activates PKR and encodes a separate function which selectively prevents the phosphorylation of at least one PKR target, eIF2alpha. The nature of this potential activator element, and how analogous cellular elements could affect PKR pathways which affect growth arrest and differentiation are discussed. Images
Mohr, I; Gluzman, Y
The genus Saccharomyces consists of several species divided into the sensu stricto and the sensu lato groups. The genomes of these species differ in the number and organization of nuclear chromosomes and in the size and organization of mitochondrial DNA (mtDNA). In the present experiments we examined whether these yeasts can exchange DNA and thereby create novel combinations of genetic material. Several putative haploid, heterothallic yeast strains were isolated from different Saccharomyces species. All of these strains secreted an a- or ?-like pheromone recognized by S. cerevisiae tester strains. When interspecific crosses were performed by mass mating between these strains, hybrid zygotes were often detected. In general, the less related the two parental species were, the fewer hybrids they gave. For some crosses, viable hybrids could be obtained by selection on minimal medium and their nuclear chromosomes and mtDNA were examined. Often the frequency of viable hybrids was very low. Sometimes putative hybrids could not be propagated at all. In the case of sensu stricto yeasts, stable viable hybrids were obtained. These contained both parental sets of chromosomes but mtDNA from only one parent. In the case of sensu lato hybrids, during genetic stabilization one set of the parental chromosomes was partially or completely lost and the stable mtDNA originated from the same parent as the majority of the nuclear chromosomes. Apparently, the interspecific hybrid genome was genetically more or less stable when the genetic material originated from phylogenetically relatively closely related parents; both sets of nuclear genetic material could be transmitted and preserved in the progeny. In the case of more distantly related parents, only one parental set, and perhaps some fragments of the other one, could be found in genetically stabilized hybrid lines. The results obtained indicate that Saccharomyces yeasts have a potential to exchange genetic material. If Saccharomyces isolates could mate freely in nature, horizontal transfer of genetic material could have occurred during the evolution of modern yeast species.
Marinoni, Gaelle; Manuel, Martine; Petersen, Randi F?ns; Hvidtfeldt, Jeanne; Sulo, Pavol; Piskur, Jure
The development of genetically marked animal tumour xenografts is an area of ongoing research to enable easier and more reliable testing of cancer therapies. Genetically marked tumour models have a number of advantages over conventional tumour models, including the easy longitudinal monitoring of therapies and the reduced number of animals needed for trials. Several different methods have been used in previous studies to mark tumours genetically, however all have limitations, such as genotoxicity and other artifacts related to the usage of integrating viral vectors. Recently, we have generated an episomally maintained plasmid DNA (pDNA) expression system based on Scaffold/Matrix Attachment Region (S/MAR), which permits long-term luciferase transgene expression in the mouse liver. Here we describe a further usage of this pDNA vector with the human Ubiquitin C promoter to create stably transfected human hepatoma (Huh7) and human Pancreatic Carcinoma (MIA-PaCa2) cell lines, which were delivered into “immune deficient” mice and monitored longitudinally over time using a bioluminometer. Both cell lines revealed sustained episomal long-term luciferase expression and formation of a tumour showing the pathological characteristics of hepatocellular carcinoma (HCC) and pancreatic carcinoma (PaCa), respectively. This is the first demonstration that a pDNA vector can confer sustained episomal luciferase transgene expression in various mouse tumour models and can thus be readily utilised to follow tumour formation without interfering with the cellular genome.
Gowers, Kate; Harbottle, Richard Paul
Real-time fluorescence imaging of viral proteins in living cells provides a valuable means to study virus-host interactions. The challenge of generating replication-competent fluorescent influenza A virus is that the segmented genome does not allow fusion of a fluorescent protein gene to any viral gene. Here, we introduced the tetracysteine (TC) biarsenical labeling system into influenza virus in order to fluorescently label viral protein in the virus life cycle. We generated infectious influenza A viruses bearing a small TC tag (CCPGCC) in the loop/linker regions of the NS1 proteins. In the background of A/Puerto Rico/8/34 (H1N1) (PR8) virus, the TC tag can be inserted into NS1 after amino acid 52 (AA52) (PR8-410), AA79 (PR8-412), or AA102 (PR8-413) or the TC tag can be inserted and replace amino acids 79 to 84 (AA79-84) (PR8-411). Although PR8-410, PR8-411, and PR8-412 viruses are attenuated than the wild-type (WT) virus to some extent in multiple-cycle infection, their growth potential is similar to that of the WT virus during a single cycle of infection, and their NS1 subcellular localization and viral protein synthesis rate are quite similar to those of the WT virus. Furthermore, labeling with membrane-permeable biarsenical dye resulted in fluorescent NS1 protein in the context of virus infection. We could exploit this strategy on NS1 protein of A/Texas/36/91 (H1N1) (Tx91) by successfully rescuing a TC-tagged virus, Tx91-445, which carries the TC tag replacement of AA79-84. The infectivity of Tx91-445 virus was similar to that of WT Tx91 during multiple cycles of replication and a single cycle of replication. The NS1 protein derived from Tx91-445 can be fluorescently labeled in living cells. Finally, with biarsenical labeling, the engineered replication-competent virus allowed us to visualize NS1 protein nuclear import in virus-infected cells in real time.
Li, Yang; Lu, Xinya; Li, Junwei; Berube, Nathalie; Giest, Kerri-Lane; Liu, Qiang; Anderson, Deborah H.; Zhou, Yan
The rapid improvements in DNA synthesis technology hold the potential to revolutionize biosciences in the near future. Traditional genetic engineering methods are template dependent and make extensive but laborious use of site-directed mutagenesis to explore the impact of small variations on an existing sequence “theme”. De novo gene and genome synthesis frees the investigator from the restrictions of the pre-existing template and allows for the rational design of any conceivable new sequence theme. Viruses, being amongst the simplest replicating entities, have been at the forefront of the advancing biosciences since the dawn of molecular biology. Viral genomes, especially those of RNA viruses, are relatively short, often less than 10,000 bases long, making them amenable to whole genome synthesis with the currently available technology. For this reason viruses are once again poised to lead the way in the budding field of synthetic biology – for better or worse.
Mueller, Steffen; Coleman, J. Robert; Wimmer, Eckard
Water-borne transmission has been suggested as an important transmission mechanism for Influenza A (IA) viruses in wild duck populations; however, relatively few studies have attempted to detect IA viruses from aquatic habitats. Water-isolated viruses have rarely been genetically characterized and evaluation for persistence in water and infectivity in natural hosts has never been documented. In this study, we focused on two IA viruses (H3N8 and H4N6 subtypes) isolated from surface lake water in Minnesota, USA. We investigated the relative prevalence of the two virus subtypes in wild duck populations at the sampling site and their genetic relatedness to IA viruses isolated in wild waterbirds in North America. Viral persistence under different laboratory conditions (temperature and pH) and replication in experimentally infected Mallards (Anas platyrhynchos) were also characterized. Both viruses were the most prevalent subtype one year following their isolation in lake water. The viruses persisted in water for an extended time period at constant temperature (several weeks) but infectivity rapidly reduced under multiple freeze-thaw cycles. Furthermore, the two isolates efficiently replicated in Mallards. The complete genome characterization supported that these isolates originated from genetic reassortments with other IA viruses circulating in wild duck populations during the year of sampling. Based on phylogenetic analyses, we couldn't identify genetically similar viruses in duck populations in the years following their isolation from lake water. Our study supports the role for water-borne transmission for IA viruses but also highlights that additional field and experimental studies are required to support inter-annual persistence in aquatic habitats.
Lebarbenchon, Camille; Yang, My; Keeler, Shamus P.; Ramakrishnan, Muthannan A.; Brown, Justin D.; Stallknecht, David E.; Sreevatsan, Srinand
It is proposed that high velocity asteroidal impacts with the Earth created polymeric nucleotide sequences out of monomeric nucleotides via direct compressive forces. The developed model describes the simultaneous formation of histone-equivalent proteins and RNA/DNA-equivalent template structures as a natural and expected consequence of bolide impactions with organic material accumulating on the crustal surface of the Earth approximately 3.8-3.5 billion years ago. It is shown that literally billions of different gene-equivalent nucleotide sequences, each one having a set of surface-complementary histone-equivalent proteins, might be created in such a manner. It is hypothesized that it is this process that gave rise to the chemical substrate upon which Darwinian selective forces have acted ever since. PMID:1614364
Brown, R D
Globalisation, in terms of the rapid and free movement of people, animals and food, has created a new paradigm, increasing the range and rate of distribution of many pathogens. In the present study, Torque teno sus viruses (TTSuVs) have been used as a model to evaluate the effects of global trade on viral heterogeneity, and how the movement of live pigs can affect the distribution and composition of virus populations. Seventeen countries from different parts of the world have been screened for TTSuV1 and TTSuvV2. High levels of genetic diversity have been found as well as two new TTSuV subtypes. A small fraction of this diversity (<5%) was related with spatial structure; however the majority (>50%) was best explained by the exchange of live pigs among countries, pointing to the direct relationship between the movement of hosts and the diversity of their accompanying viruses. Taking TTSuVs as sentinels, this study revealed that the distribution and diversity of comensal microflora in live animals subjected to global trade is shaped by the commercial movements among countries. In the case of TTSuVs, it appears that commercial movements of animals are eroding the genetic composition of the virus populations that may have been present in pig herds since their domestication. PMID:22101091
Cortey, Martí; Pileri, Emanuela; Segalés, Joaquim; Kekarainen, Tuija
Pathogen-host interaction studies have demonstrated the importance of host factors in the pathogenesis of infectious disease. An emerging theme is that polymorphisms in the genes encoding these factors can influence the host response to infection and the course of disease. Genetic variation affecting interferon lambda (IFN-?) expression is now known to influence the outcome of both hepatitis C virus and herpes simplex virus type 1 infection in humans. IFN-? is expressed at higher levels in organs with high epithelial cell content such as the respiratory and gastrointestinal tracts. Interestingly, data from animal models show that IFN-? contributes to host control of viruses infecting these sites, including influenza A virus, severe acute respiratory syndrome coronavirus, and rotavirus. Furthermore, defective IFN-? production by humans with asthma impairs the control of rhinovirus infection. We hypothesize that genetic variation of IFN-? could potentially influence the course of disease during infection with many viruses that infect epithelial cells. PMID:24329419
Russell, Clark D; Griffiths, Samantha J; Haas, Jürgen
The Japanese encephalitis virus (JEV), an arthropod-born Flavivirus, is the major cause of viral encephalitis, responsible for 10,000–15,000 deaths each year, yet is a neglected tropical disease. Since the JEV distribution area has been large and continuously extending toward new Asian and Australasian regions, it is considered an emerging and reemerging pathogen. Despite large effective immunization campaigns, Japanese encephalitis remains a disease of global health concern. JEV zoonotic transmission cycles may be either wild or domestic: the first involves wading birds as wild amplifying hosts; the second involves pigs as the main domestic amplifying hosts. Culex mosquito species, especially Cx. tritaeniorhynchus, are the main competent vectors. Although five JEV genotypes circulate, neither clear-cut genotype-phenotype relationship nor clear variations in genotype fitness to hosts or vectors have been identified. Instead, the molecular epidemiology appears highly dependent on vectors, hosts' biology, and on a set of environmental factors. At global scale, climate, land cover, and land use, otherwise strongly dependent on human activities, affect the abundance of JEV vectors, and of wild and domestic hosts. Chiefly, the increase of rice-cultivated surface, intensively used by wading birds, and of pig production in Asia has provided a high availability of resources to mosquito vectors, enhancing the JEV maintenance, amplification, and transmission. At fine scale, the characteristics (density, size, spatial arrangement) of three landscape elements (paddy fields, pig farms, human habitations) facilitate or impede movement of vectors, then determine how the JEV interacts with hosts and vectors and ultimately the infection risk to humans. If the JEV is introduced in a favorable landscape, either by live infected animals or by vectors, then the virus can emerge and become a major threat for human health. Multidisciplinary research is essential to shed light on the biological mechanisms involved in the emergence, spread, reemergence, and genotypic changes of JEV.
Le Flohic, Guillaume; Porphyre, Vincent; Gonzalez, Jean-Paul
The aim of this study was to investigate whether observed time-until-death of Atlantic cod (Gadus morhua L.) juveniles in separate challenge tests with Vibrio anguillarum (causes vibriosis) and nodavirus [causes viral nervous necrosis (VNN)] are due to differences in susceptibility (whether at risk or not) or increased endurance (individual hazard, given that the animal is susceptible) using a cure mixture (CURE) model with Gibbs sampling. Observed time-until-death, prepared as sequential binary records, were analyzed with the CURE model and results were compared with cross-sectional threshold (SIMPLE) and an ordinary longitudinal survival score (NAÏVE) model (i.e., assuming that all animals are susceptible). Overall mortality at the end of the test was 86 and 71% for vibriosis and VNN, respectively. But the CURE model estimated 92 and 82% of the population to be susceptible to vibriosis and VNN, respectively. Hence, a substantial fraction among the survivors were considered to be susceptible but with high endurance. The underlying heritability of susceptibility was moderate for vibriosis (0.33) and extremely high for VNN (0.91), somewhat greater compared with classical SIMPLE model (0.19 and 0.76 for vibriosis and VNN, respectively), analyzing end survival as a cross-sectional binary trait. Estimates of the underlying heritability were low for single test-day scores of both endurance (0.02 and 0.15 for vibriosis and VNN, respectively) in the CURE model and for the NAÏVE model (0.02 and 0.18 for vibriosis and VNN, respectively). Based on the CURE model, the genetic correlation between susceptibility and endurance was low to moderately positive and significantly different from unity (P < 0.01) for both vibriosis (0.13) and VNN (0.47). Estimated breeding values from the SIMPLE and NAÏVE models showed moderate to high correlations (0.41 to 0.96) with EBV for susceptibility and endurance in the CURE model. The analyses indicate that susceptibility and endurance are apparently distinct genetic traits. Still, the genetic variation estimated in the SIMPLE and NAÏVE models seems to a large extent to be controlled by susceptibility and an efficient genetic selection for reduced susceptibility to vibriosis and VNN is therefore likely feasible even when using classical (noncure) models. Earlier termination of the challenge test or back truncation of survival data is not recommended as this likely shifts the focus of selection towards endurance rather than susceptibility. PMID:23736060
Bangera, R; Ødegård, J; Nielsen, H M; Gjøen, H M; Mortensen, A
Classical swine fever (CSF)-like symptoms in pigs regarded as free from CSF has been reported previously. From sick pigs with CSF-like symptoms, and who had been inoculated with the hog cholera vaccine, samples were collected and subjected to RT-PCR using specific primers. Twelve bovine viral diarrhea virus 2 (BVDV-2) strains were screened and isolated. Homology comparison showed that the E2 genes of the twelve isolates were highly conserved. The genome of the one of the BVDV-2 isolates (named as SH-28) from the sick pigs, which showed a noncytopathic effect in MDBK cell cultures and strong reactivity with monoclonal antibody (MAb) Bz-53 raised against BVDV-2, was sequenced. The genome of SH-28 comprises 12,279 nucleotides and contains a large open reading frame beginning at nucleotide 386 and ending at nucleotide 12,073. Genomic comparison and phylogenetic analyzes showed that SH-28 fall into BVDV-2 subtype and was most similar to XJ-04 (nucleotide and amino acid homologies were 89.9-93.8 % and 91.1-96.9 %, respectively), but was genetically divergent from ZM-95 (pig BVDV-1). PMID:23085884
Tao, Jie; Wang, Yin; Wang, Juan; Wang, Jian-ye; Zhu, Guo-qiang
Directed open reading frame (ORF) disruption and a serial selection technique in Escherichia coli and the extremely thermophilic archaeon Sulfolobus solfataricus allowed the identification of otherwise cryptic crucial and noncrucial viral open reading frames in the genome of the archaeal virus SSV1. It showed that the 15. 5-kbp viral genome can incorporate a 2.96-kbp insertion without loss of viral function and package this DNA properly into infectious virus particles. The selection technique, based on the preferential binding of ethidium bromide to relaxed DNA and the resulting inhibition of endonuclease cleavage to generate a pool of mostly singly cut molecules, should be generally applicable. A fully functional viral shuttle vector for S. solfataricus and E. coli was made. This vector spreads efficiently through infected cultures of S. solfataricus, its replication is induced by UV irradiation, it forms infectious virus particles, and it is stable at high copy number in both S. solfataricus and E. coli. The classification of otherwise unidentifiable ORFs in SSV1 facilitates genetic analysis of this virus, and the shuttle vector should be useful for the development of genetic systems for Crenarchaeota.
Stedman, K M; Schleper, C; Rumpf, E; Zillig, W
Satellite RNAs usually lack substantial homology with their helper viruses. The 356-nucleotide satC of Turnip crinkle virus (TCV) is unusual in that its 3?-half shares high sequence similarity with the TCV 3? end. Computer modeling, structure probing, and/or compensatory mutagenesis identified four hairpins and three pseudoknots in this TCV region that participate in replication and/or translation. Two hairpins and two pseudoknots have been confirmed as important for satC replication. One portion of the related 3? end of satC that remains poorly characterized corresponds to juxtaposed TCV hairpins H4a and H4b and pseudoknot ?3, which are required for the TCV-specific requirement of translation (V. A. Stupina et al., RNA 14:2379-2393, 2008). Replacement of satC H4a with randomized sequence and scoring for fitness in plants by in vivo genetic selection (SELEX) resulted in winning sequences that contain an H4a-like stem-loop, which can have additional upstream sequence composing a portion of the stem. SELEX of the combined H4a and H4b region in satC generated three distinct groups of winning sequences. One group models into two stem-loops similar to H4a and H4b of TCV. However, the selected sequences in the other two groups model into single hairpins. Evolution of these single-hairpin SELEX winners in plants resulted in satC that can accumulate to wild-type (wt) levels in protoplasts but remain less fit in planta when competed against wt satC. These data indicate that two highly distinct RNA conformations in the H4a and H4b region can mediate satC fitness in protoplasts.
Guo, Rong; Lin, Wai; Zhang, Jiuchun; Simon, Anne E.; Kushner, David B.
The objective of this research is to analyze the genetic characterization of a bovine viral diarrhea virus (BVDV) strain (HB-DCZ\\u000a strain) isolated from China and describe its relationship with other BVDV strains. Special primers (forward: 5?-gagatctcgggaggtac-3?,\\u000a reverse: 5?-cctctcggcatgatcccgaaa-3?) are used to amplify partial NS2–3 sequence of HB-DCZ strain by reverse transcription polymerase chain reaction (RT-PCR). The product of PCR is
Yuelan Zhao; Jianhua Qin; Hongbin Guo; Yuzhu Zuo; Baoning Zhang; Lei Zhang
Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated\\u000a IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics\\u000a system was developed to generate a recombinant VHSV
Arun Ammayappan; Gael Kurath; Tarin M. Thompson; Vikram N. Vakharia
The Kaposi's sarcoma-associated herpesvirus gene products K3 and K5 are viral ubiquitin E3 ligases which downregulate MHC-I and additional cell surface immunoreceptors. To identify novel cellular genes required for K5 function we performed a forward genetic screen in near-haploid human KBM7 cells. The screen identified proteolipid protein 2 (PLP2), a MARVEL domain protein of unknown function, as essential for K5 activity. Genetic loss of PLP2 traps the viral ligase in the endoplasmic reticulum, where it is unable to ubiquitinate and degrade its substrates. Subsequent analysis of the plasma membrane proteome of K5-expressing KBM7 cells in the presence and absence of PLP2 revealed a wide range of novel K5 targets, all of which required PLP2 for their K5-mediated downregulation. This work ascribes a critical function to PLP2 for viral ligase activity and underlines the power of non-lethal haploid genetic screens in human cells to identify the genes involved in pathogen manipulation of the host immune system.
Timms, Richard T.; Duncan, Lidia M.; Tchasovnikarova, Iva A.; Antrobus, Robin; Smith, Duncan L.; Dougan, Gordon; Weekes, Michael P.; Lehner, Paul J.
Recovery from acute hepatitis B virus (HBV) infection requires a broad, vigorous T-cell response, which is enhanced in mice when chemokine receptor 5 (CCR5) is missing. To test the hypothesis that production of a nonfunctional CCR5 (CCR5?32 [a functionally null allele containing a 32-bp deletion]) increases the likelihood of recovery from hepatitis B in humans, we studied 526 persons from three cohorts in which one person with HBV persistence was matched to two persons who recovered from an HBV infection. Recovery or persistence was determined prior to availability of lamivudine. We determined genotypes for CCR5?32 and for polymorphisms in the CCR5 promoter and in coding regions of the neighboring genes, chemokine receptor 2 (CCR2) and chemokine receptor-like 2 (CCRL2). Allele and haplotype frequencies were compared among the 190 persons with viral recovery and the 336 with persistence by use of conditional logistic regression. CCR5?32 reduced the risk of developing a persistent HBV infection by nearly half (odds ratio [OR], 0.53; 95% confidence interval [CI], 0.33 to 0.83; P = 0.006). This association was virtually identical in persons with and without a concomitant human immunodeficiency virus infection. Of the nine individuals who were homozygous for the deletion, eight recovered from infection (OR, 0.25; 95% CI, 0.03 to 1.99; P = 0.19). None of the other neighboring polymorphisms examined were associated with HBV outcome. These data demonstrate a protective effect of CCR5?32 in recovery from an HBV infection, provide genetic epidemiological evidence for a role of CCR5 in the immune response to HBV, and suggest a potential therapeutic treatment for patients persistently infected with HBV.
Thio, Chloe L.; Astemborski, Jacquie; Bashirova, Arman; Mosbruger, Timothy; Greer, Spencer; Witt, Mallory D.; Goedert, James J.; Hilgartner, Margaret; Majeske, Audrey; O'Brien, Stephen J.; Thomas, David L.; Carrington, Mary
The industrial use of various kinds of rubber-like (hyper-elastic) material is rapidly increasing and growing in importance, especially in automobiles, trains, and machinery(1). In the past, rubber engineers and designers have predicted the behavior of rubber-like materials using analytic methods for limited problems or approximate methods for general problems. Yet, with the progress of digital computers, finite element methods(2), represented by the Mooney-Rivlin model, are now widely used to analyze hyper-elastic as well as isotropic materials. The conventional method used to evaluate the properties of rubber-like materials is the least square method (LSM), however, this method has a low precision and involves a tedious pre-solving process. Accordingly, this study proposes a simple yet powerful method for estimating the properties of rubber-like materials using a successive zooming genetic algorithm (SZGA). The proposed method results in dependable and precise rubber-like properties for various Mooney-Rivlin models based on simply changing the objective function. To demonstrate the effectiveness of the proposed method, it is compared with Haines & Wilson's method (LSM) and other commercial packages.
Kwon, Young-Doo; Kwon, Hyun-Wook; Kim, Wha-Jung; Yeo, Sim-Dong
To evaluate human immunodeficiency virus type 1 (HIV-1) replication and selection of drug-resistant viruses during seemingly effective highly active antiretroviral therapy (HAART), multiple HIV-1 env and pol sequences were analyzed and viral DNA levels were quantified from nucleoside analog-experienced children prior to and during a median of 5.1 (range, 1.8 to 6.4) years of HAART. Viral replication was detected at
Lisa M. Frenkel; Yang Wang; Gerald H. Learn; Jennifer L. McKernan; Giovanina M. Ellis; Kathleen M. Mohan; Sarah E. Holte; Shannon M. De Vange; Diane M. Pawluk; Ann J. Melvin; Paul F. Lewis; Laura M. Heath; Ingrid A. Beck; Madhumita Mahalanabis; Wilscott E. Naugler; Nicole H. Tobin; James I. Mullins
Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-?NV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-?NV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-?NV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines.
Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M.; Vakharia, Vikram N.
Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry.
Pinheiro, Vitor B.; Holliger, Philipp
Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry. PMID:24745974
Pinheiro, Vitor B; Holliger, Philipp
HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10?12). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the ‘intermediate phenotype’ nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host–pathogen interaction. DOI: http://dx.doi.org/10.7554/eLife.01123.001
Bartha, Istvan; Carlson, Jonathan M; Brumme, Chanson J; McLaren, Paul J; Brumme, Zabrina L; John, Mina; Haas, David W; Martinez-Picado, Javier; Dalmau, Judith; Lopez-Galindez, Cecilio; Casado, Concepcion; Rauch, Andri; Gunthard, Huldrych F; Bernasconi, Enos; Vernazza, Pietro; Klimkait, Thomas; Yerly, Sabine; O'Brien, Stephen J; Listgarten, Jennifer; Pfeifer, Nico; Lippert, Christoph; Fusi, Nicolo; Kutalik, Zoltan; Allen, Todd M; Muller, Viktor; Harrigan, P Richard; Heckerman, David; Telenti, Amalio; Fellay, Jacques
The present invention provides novel recombinant baculovirus expression systems for expressing foreign genetic material in a host cell. Such expression systems are readily adapted to an automated method for expression foreign genetic material in a high throughput manner. In other aspects, the present invention features a novel automated method for determining the function of foreign genetic material by transfecting the same into a host by way of the recombinant baculovirus expression systems according to the present invention.
Clark, Robin (Benecia, CA); Davies, Anthony (Mill Valley, CA)
An imported carrier stallion (A) from Europe was implicated in causing an extensive outbreak of equine viral arteritis (EVA) on a Warmblood breeding farm in Pennsylvania, USA. Strains of equine arteritis virus (EAV) present in the semen of two carrier stallions (A and G) on the farm were compared to those in tissues of foals born during the outbreak, as
Udeni B. R. Balasuriya; Jodi F. Hedges; Steven A. Nadler; William H. McCollum; Peter J. Timoney; N. James MacLachlan
Genetic typing of bovine viral diarrhea virus (BVDV) has distinguished BVDV-1 and BVDV-2 species and an emerging putative third species (HoBi-like virus), recently detected in southern Italy, signaling the occurrence of natural infection in Europe. Recognizing the need to update the data on BVDV genetic variability in Italy for mounting local and European alerts, a wide collection of 5? UTR sequences (n = 371) was selected to identify the frequency of genotypes and subtypes at the herd level. BVDV-1 had the highest frequency, followed by sporadic BVDV-2. No novel HoBi-like viruses were identified. Four distribution patterns of BVDV-1 subtypes were observed: highly prevalent subtypes with a wide temporal-spatial distribution (1b and 1e), low prevalent subtypes with a widespread geographic distribution (1a, 1d, 1g, 1h, and 1k) or a restricted geographic distribution (1f), and sporadic subtypes detected only in single herds (1c, 1j, and 1l). BVDV-1c, k, and l are reported for the first time in Italy. A unique genetic variant was detected in the majority of herds, but cocirculation of genetic variants was also observed. Northern Italy ranked first for BVDV introduction, prevalence, and dispersion. Nevertheless, the presence of sporadic variants in other restricted areas suggests the risk of different routes of BVDV introduction.
Lauzi, Stefania; Ebranati, Erika; Giammarioli, Monica; Cannella, Vincenza; Masoero, Loretta; Canelli, Elena; Guercio, Annalisa; Caruso, Claudio; Ciccozzi, Massimo; De Mia, Gian Mario; Acutis, Pier Luigi; Zehender, Gianguglielmo
Nonstructural protein 5A (NS5A) of bovine viral diarrhea virus (BVDV) is a hydrophilic phosphoprotein with RNA binding activity and a critical component of the viral replicase. In silico analysis suggests that NS5A encompasses three domains interconnected by two low-complexity sequences (LCSs). While domain I harbors two functional determinants, an N-terminal amphipathic helix important for membrane association, and a Zn-binding site essential for RNA replication, the structure and function of the C-terminal half of NS5A are still ill defined. In this study, we introduced a panel of 10 amino acid deletions covering the C-terminal half of NS5A. In the context of a highly efficient monocistronic replicon, deletions in LCS I and the N-terminal part of domain II, as well as in domain III, were tolerated with regard to RNA replication. When introduced into a bicistronic replicon, only deletions in LCS I and the N-terminal part of domain II were tolerated. In the context of the viral full-length genome, these mutations allowed residual virion morphogenesis. Based on these data, a functional monocistronic BVDV replicon coding for an NS5A variant with an insertion of the fluorescent protein mCherry was constructed. Live cell imaging demonstrated that a fraction of NS5A-mCherry localizes to the surface of lipid droplets. Taken together, this study provides novel insights into the functions of BVDV NS5A. Moreover, we established the first pestiviral replicon expressing fluorescent NS5A-mCherry to directly visualize functional viral replication complexes by live cell imaging.
Isken, Olaf; Langerwisch, Ulrike; Schonherr, Robert; Lamp, Benjamin; Schroder, Kristin; Duden, Rainer; Rumenapf, Tillmann H.
Information on global human movement patterns is central to spatial epidemiological models used to predict the behavior of influenza and other infectious diseases. Yet it remains difficult to test which modes of dispersal drive pathogen spread at various geographic scales using standard epidemiological data alone. Evolutionary analyses of pathogen genome sequences increasingly provide insights into the spatial dynamics of influenza viruses, but to date they have largely neglected the wealth of information on human mobility, mainly because no statistical framework exists within which viral gene sequences and empirical data on host movement can be combined. Here, we address this problem by applying a phylogeographic approach to elucidate the global spread of human influenza subtype H3N2 and assess its ability to predict the spatial spread of human influenza A viruses worldwide. Using a framework that estimates the migration history of human influenza while simultaneously testing and quantifying a range of potential predictive variables of spatial spread, we show that the global dynamics of influenza H3N2 are driven by air passenger flows, whereas at more local scales spread is also determined by processes that correlate with geographic distance. Our analyses further confirm a central role for mainland China and Southeast Asia in maintaining a source population for global influenza diversity. By comparing model output with the known pandemic expansion of H1N1 during 2009, we demonstrate that predictions of influenza spatial spread are most accurate when data on human mobility and viral evolution are integrated. In conclusion, the global dynamics of influenza viruses are best explained by combining human mobility data with the spatial information inherent in sampled viral genomes. The integrated approach introduced here offers great potential for epidemiological surveillance through phylogeographic reconstructions and for improving predictive models of disease control. PMID:24586153
Lemey, Philippe; Rambaut, Andrew; Bedford, Trevor; Faria, Nuno; Bielejec, Filip; Baele, Guy; Russell, Colin A; Smith, Derek J; Pybus, Oliver G; Brockmann, Dirk; Suchard, Marc A
Information on global human movement patterns is central to spatial epidemiological models used to predict the behavior of influenza and other infectious diseases. Yet it remains difficult to test which modes of dispersal drive pathogen spread at various geographic scales using standard epidemiological data alone. Evolutionary analyses of pathogen genome sequences increasingly provide insights into the spatial dynamics of influenza viruses, but to date they have largely neglected the wealth of information on human mobility, mainly because no statistical framework exists within which viral gene sequences and empirical data on host movement can be combined. Here, we address this problem by applying a phylogeographic approach to elucidate the global spread of human influenza subtype H3N2 and assess its ability to predict the spatial spread of human influenza A viruses worldwide. Using a framework that estimates the migration history of human influenza while simultaneously testing and quantifying a range of potential predictive variables of spatial spread, we show that the global dynamics of influenza H3N2 are driven by air passenger flows, whereas at more local scales spread is also determined by processes that correlate with geographic distance. Our analyses further confirm a central role for mainland China and Southeast Asia in maintaining a source population for global influenza diversity. By comparing model output with the known pandemic expansion of H1N1 during 2009, we demonstrate that predictions of influenza spatial spread are most accurate when data on human mobility and viral evolution are integrated. In conclusion, the global dynamics of influenza viruses are best explained by combining human mobility data with the spatial information inherent in sampled viral genomes. The integrated approach introduced here offers great potential for epidemiological surveillance through phylogeographic reconstructions and for improving predictive models of disease control.
Lemey, Philippe; Rambaut, Andrew; Bedford, Trevor; Faria, Nuno; Bielejec, Filip; Baele, Guy; Russell, Colin A.; Smith, Derek J.; Pybus, Oliver G.; Brockmann, Dirk; Suchard, Marc A.
Latently infecting viruses are an important class of virus that plays a key role in viral evolution and human health. Here we report a genome-scale forward-genetics screen for host-dependencies of the latently-infecting bacteriophage lambda. This screen identified 57 Escherichia coli (E. coli) genes—over half of which have not been previously associated with infection—that when knocked out inhibited lambda phage's ability to replicate. Our results demonstrate a highly integrated network between lambda and its host, in striking contrast to the results from a similar screen using the lytic-only infecting T7 virus. We then measured the growth of E. coli under normal and infected conditions, using wild-type and knockout strains deficient in one of the identified host genes, and found that genes from the same pathway often exhibited similar growth dynamics. This observation, combined with further computational and experimental analysis, led us to identify a previously unannotated gene, yneJ, as a novel regulator of lamB gene expression. A surprising result of this work was the identification of two highly conserved pathways involved in tRNA thiolation—one pathway is required for efficient lambda replication, while the other has anti-viral properties inhibiting lambda replication. Based on our data, it appears that 2-thiouridine modification of tRNAGlu, tRNAGln, and tRNALys is particularly important for the efficient production of infectious lambda phage particles.
Maynard, Nathaniel D.; Birch, Elsa W.; Sanghvi, Jayodita C.; Chen, Lu; Gutschow, Miriam V.; Covert, Markus W.
Background Hepatic steatosis in HCV patients has been postulated as a risk factor associated with a higher frequency of fibrosis and cirrhosis. A single genetic variant, PNPLA3 I148M, has been widely associated with increased hepatic steatosis. Previous studies of the PNPLA3 I148M sequence variant in HCV infected individuals have reported an association between this variant and prevalence of steatosis, fibrosis, and cirrhosis. To evaluate the impact of PNPLA3 I148M variant on metabolic traits and treatment response in HCV genotype 2 and 3 infected patients. Methods Three hundred and eighty-two treatment naïve HCV genotype 2 or 3 infected patients were included in a phase III, open label, randomized, multicenter, investigator-initiated trial (the NORDynamIC study), in which pretreatment liver biopsies were mandatory. PNPLA3I148M genotyping was performed in a total of 359 Caucasian patients. Results In HCV genotype 2 infected patients carrying the PNPLA3 148M allele, there was significantly increased insulin resistance (P?=?0.023) and lower viral load (P?=?0.005) at baseline as well as the first seven days of antiviral treatment. These results were not observed in HCV genotype 3 infected patients. Conclusions Our results suggest a possible association between the PNPLA3 148M allele and insulin resistance as well as baseline viral load in HCV genotype 2, but not in genotype 3.
Genetic predisposition factors and nasopharyngeal carcinoma risk: a review of epidemiological association studies, 2000-2011: Rosetta Stone for NPC: genetics, viral infection, and other environmental factors.
While infection with Epstein-Barr virus (EBV) is known to be an essential risk factor for the development of nasopharyngeal carcinoma (NPC), other co-factors including genetic factors are thought to play an important role. In this review, we summarize association studies conducted over the past decade to evaluate the role of genetic polymorphisms in NPC development. A review of the literature identified close to 100 studies, including 3 genome-wide association studies (GWAS), since 2000 that evaluated genetic polymorphisms and NPC risk in at least 100 NPC cases and 100 controls. Consistent evidence for associations were reported for a handful of genes, including immune-related HLA Class I genes, DNA repair gene RAD51L1, cell cycle control genes MDM2 and TP53, and cell adhesion/migration gene MMP2. However, for most of the genes evaluated, there was no effort to replicate findings and studies were largely modest in size, typically consisting of no more than a few hundred cases and controls. The small size of most studies, and the lack of attempts at replication have limited progress in understanding the genetics of NPC. Moving forward, if we are to advance our understanding of genetic factors involved in the development of NPC, and of the impact of gene-gene and gene-environment interations in the development of this disease, consortial efforts that pool across multiple, well-designed and coordinated efforts will most likely be required. PMID:22300735
Hildesheim, Allan; Wang, Cheng-Ping
Using Genetic Algorithm to optimize mechanical properties of ceramic die material, the best volume fraction of each mechanical property can be obtained respectively. And the best volume fraction of comprehensive mechanical properties also can be obtained by multi-objective optimization. Experimental results of the material fabrication indicate that the developed ceramic material possesses good comprehensive mechanical properties when the volume fraction
Jingjie Zhang; Chonghai Xu
The vast majority of the human experience with viral infections is associated with acute symptoms, such as malaise, fever, chills, rhinitis and diarrhea. With this acute or lytic phase, the immune system mounts a response and eliminates the viral agent while acquiring antibodies to that specific viral subtype. With latent or chronic infections, the viral agent becomes incorporated into the human genome. Viral agents capable of integration into the host's genetic material are particularly dangerous and may commandeer the host's ability to regulate normal cell growth and proliferation. The oncogenic viruses may immortalize the host cell, and facilitate malignant transformation. Cell growth and proliferation may be enhanced by viral interference with tumor suppressor gene function (p53 and pRb). Viruses may act as vectors for mutated proto-oncogenes (oncogenes). Overexpression of these oncogenes in viral-infected cells interferes with normal cell function and allows unregulated cell growth and proliferation, which may lead to malignant transformation and tumour formation. Development of oral neoplasms, both benign and malignant, has been linked to several viruses. Epstein-Barr virus is associated with oral hairy leukoplakia, lymphoproliferative disease, lymphoepithelial carcinoma, B-cell lymphomas, and nasopharyngeal carcinoma. Human herpesvirus-8 has been implicated in all forms of Kaposi's sarcoma, primary effusion lymphomas, multiple myeloma, angioimmunoblastic lymphadenopathy, and Castleman's disease. Human herpesvirus-6 has been detected in lymphoproliferative disease, lymphomas, Hodgkin's disease, and oral squamous cell carcinoma. The role of human papillomavirus in benign (squamous papilloma, focal epithelial hyperplasia, condyloma acuminatum, verruca vulgaris), premalignant (oral epithelial dysplasia), and malignant (squamous cell carcinoma) neoplasms within the oral cavity is well recognized. Herpes simplex virus may participate as a cofactor in oral squamous cell carcinoma development by enhancing activation, amplification, and overexpression of pre-existing oncogenes within neoplastic tissues. Because of the integral role of viruses in malignant transformation of host cells, innovative antiviral therapy may prevent tumour development, involute neoplastic proliferations, or arrest malignant progression. PMID:9930354
Flaitz, C M; Hicks, M J
The laboratory strain of murine cytomegalovirus (MCMV), K181, has been successfully engineered as a vaccine expressing murine zona pellucida 3 (mZP3) for viral vectored immunocontraception (VVIC) in mice. However, certain laboratory strains of mice are resistant to infection with K181 and therefore demonstrate resistance to VVIC. Cmv1 is the best characterised innate resistance mechanism to MCMV and was first described in C57BL/6 mice. Resistance in C57BL/6 mice is due to early and strong activation of natural killer (NK) cells by an MCMV gene product, m157, that binds directly to the NK cell activating receptor Ly49H. In this study a wild strain of MCMV, G4, which expresses a variant m157 incapable of activating Ly49H, was engineered to express murine zona pellucida 3 (mZP3) and assessed for its ability to sterilise female C57BL/6 mice. When infected with K181-mZP3 female C57BL/6 mice remained fully fertile. In contrast, female C57BL/6 mice were sterilised by a single intraperitoneal inoculation of G4-mZP3. Infertility was induced by G4-mZP3 in three strains of mice that express Ly49H, on two different histocompatibility-2 (H-2) backgrounds. Finally, enhanced immunocontraception was observed in mice expressing H-2(k) mediated resistance to MCMV when infected with G4-mZP3 compared to K181-mZP3. These data indicate that when using viral vaccine vectors, variant vector strains may be used to circumvent powerful innate immune responses against the vector and promote effective vaccination. This study highlights the importance of vaccine vector genetics in vaccination strategies. PMID:19591797
Nikolovski, Sonia; Lloyd, Megan L; Harvey, Nicole; Hardy, Christopher M; Shellam, Geoffrey R; Redwood, Alec J
Background Genetic predisposition to scrapie in sheep is associated with several variations in the peptide sequence of the prion protein gene (PRNP). DNA-based tests for scoring PRNP codons are essential tools for eradicating scrapie and for evaluating rare alleles for increased resistance to disease. In addition to those associated with scrapie, there are dozens more PRNP polymorphisms that may occur in various flocks. If not accounted for, these sites may cause base-pair mismatching with oligonucleotides used in DNA testing. Thus, the fidelity of scrapie genetic testing is enhanced by knowing the position and frequency of PRNP polymorphisms in targeted flocks. Results An adaptive DNA sequencing strategy was developed to determine the 771 bp PRNP coding sequence for any sheep and thereby produce a consensus sequence for targeted flocks. The strategy initially accounted for 43 known polymorphisms and facilitates the detection of unknown polymorphisms through an overlapping amplicon design. The strategy was applied to 953 sheep DNAs from multiple breeds in U.S. populations. The samples included two sets of reference sheep: one set for standardizing PRNP genetic testing and another set for discovering polymorphisms, estimating allele frequencies, and determining haplotype phase. DNA sequencing revealed 16 previously unreported polymorphisms, including a L237P variant on the F141 haplotype. Two mass spectrometry multiplex assays were developed to score five codons of interest in U.S. sheep: 112, 136, 141, 154, and 171. Reference tissues, DNA, trace files, and genotypes from this project are publicly available for use without restriction. Conclusion Identifying ovine PRNP polymorphisms in targeted flocks is critical for designing efficient scrapie genetic testing systems. Together with reference DNA panels, this information facilitates training, certification, and development of new tests and knowledge that may expedite the eradication of sheep scrapie.
Hantaviruses, family Bunyaviridae, are rodent-borne RNA viruses that have caused cases of hantavirus cardiopulmonary syndrome (HCPS) in various regions of the Americas. There are five hantaviral lineages associated with HCPS in Brazil: Juquitiba virus (JUQV), Araraquara virus (ARAV), Laguna Negra-like virus (LNV), Castelo dos Sonhos virus (CASV), and Anajatuba virus (ANAJV). Three additional hantaviruses have been described in rodents alone: Rio Mearim virus, Jaborá virus, and a hantavirus lineage related to Seoul virus. This study describes the genetic detection and characterization of a Juquitiba-like hantavirus in Oligoryzomys nigripes, or the black-footed pygmy rice rat, in the Serra dos Orgãos National Park, Rio de Janeiro State, where so far no cases of HCPS have been reported. PMID:19660427
Oliveira, R C; Teixeira, B R; Mello, F C A; Pereira, A P; Duarte, A S; Bonaldo, M C; Bonvicino, C R; D'Andrea, P S; Lemos, E R S
The sensitivities of DNA analytic methods have increased dramatically in the past several years. Use of such tests to analyze an individual`s genome could reveal parental origin or provide forensic evidence, as well as determine an individual`s complement of normal and abnormal genes. Some of the abnormal genes detected cause diseases in infancy, while the effects of others may become manifest only in adulthood. Finally, detection of specific, acquired genomic changes may indicate increased susceptibility to or herald the onset of certain malignancies. Many health professionals as well as lay people may not appreciate how frequently biological samples are stored and how easily samples that have been stored for an unrelated reason could be used for genetic analysis in the future. The potential problems posed by such uses were explored at length in a Workshop sponsored by the National Center for Human Genome Research and the Centers for Diseases Control and Prevention. ACMG members, recognizing these issues, may have concerns about access by insurers, employers, and others to samples or test results. Developing practices to be used at the time samples are obtained could alleviate problems that might arise in the future as the breadth and scope or potential genetic analyses increase. 6 refs.
Post-transplant lymphoproliferative disorders (PTLD) are a life-threatening complication of solid organ transplantation or, more rarely, hematopoietic stem cell transplantation. The majority of PTLD is of B-cell origin and associated with Epstein–Barr virus (EBV) infection. PTLD generally display involvement of extranodal sites, aggressive histology and aggressive clinical behavior. The molecular pathogenesis of PTLD involves infection by oncogenic viruses, namely EBV, as well as genetic or epigenetic alterations of several cellular genes. At variance with lymphoma arising in immunocompetent hosts, whose genome is relatively stable, a fraction of PTLD are characterized by microsatellite instability as a consequence of defects in the DNA mismatch repair mechanism. Apart from microsatellite instability, molecular alterations of cellular genes recognized in PTLD include alterations of cMYC, BCL6, TP53, DNA hypermethylation, and aberrant somatic hypermutation of protooncogenes. The occurrence of IGV mutations in the overwhelming majority of PTLD documents that malignant transformation targets germinal centre (GC) B-cells and their descendants both in EBV–positive and EBV–negative cases. Analysis of phenotypic markers of B-cell histogenesis, namely BCL6, MUM1 and CD138, allows further distinction of PTLD histogenetic categories. PTLD expressing the BCL6+/MUM1+/-/CD138? profile reflect B-cells actively experiencing the GC reaction, and comprise diffuse large B-cell lymphoma (DLBCL) centroblastic and Burkitt lymphoma. PTLD expressing the BCL6?/MUM1+/CD138? phenotype putatively derive from B-cells that have concluded the GC reaction, and comprise the majority of polymorphic PTLD and a fraction of DLBCL immunoblastic. A third group of PTLD is reminiscent of post-GC and preterminally differentiated B-cells that show the BCL6?/MUM1+/CD138+ phenotype, and are morphologically represented by either polymorphic PTLD or DLBCL immunoblastic.
Capello, Daniela; Gaidano, Gianluca
Several nanoparticle platforms are currently being developed for applications in medicine, including both synthetic materials and naturally-occurring bionanomaterials such as viral nanoparticles (VNPs) and their genome-free counterparts, virus-like particles (VLPs). A broad range of genetic and chemical engineering methods have been established that allow VNP/VLP formulations to carry large payloads of imaging reagents or drugs. Furthermore, targeted VNPs and VLPs can be generated by including peptide ligands on the particle surface. In this article, we highlight state-of-the-art virus engineering principles and discuss recent advances that bring potential biomedical applications a step closer. Viral nanotechnology has now come of age and it will not be long before these formulations assume a prominent role in the clinic.
Yildiz, Ibrahim; Shukla, Sourabh; Steinmetz, Nicole F.
For many viruses, the ability to infect eukaryotic cells depends on their transport through the cytoplasm and across the nuclear membrane of the host cell. During this journey, viral contents are biochemically processed into complexes capable of both nuclear penetration and genomic integration. We develop a stochastic model of viral entry that incorporates all relevant aspects of transport, including convection along microtubules, biochemical conversion, degradation, and nuclear entry. Analysis of the nuclear infection probabilities in terms of the transport velocity, degradation, and biochemical conversion rates shows how certain values of key parameters can maximize the nuclear entry probability of the viral material. The existence of such “optimal” infection scenarios depends on the details of the biochemical conversion process and implies potentially counterintuitive effects in viral infection, suggesting new avenues for antiviral treatment. Such optimal parameter values provide a plausible transport-based explanation of the action of restriction factors and of experimentally observed optimal capsid stability. Finally, we propose a new interpretation of how genetic mutations unrelated to the mechanism of drug action may nonetheless confer novel types of overall drug resistance.
D'Orsogna, Maria R.; Chou, Tom
Background When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA. Results This management method, which detects the ‘purest’ individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period. Conclusions Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach.
A possible act of industrial espionage is the backdrop for this case study, which introduces students to analytical techniques routinely used in most areas of biotechnology, including forensic science and paternity suits. In this fictional case, "Roger Wezel," formerly employed at ExOil developing soybean seeds high in oleic acid, now works at a competing company, SeedGene Inc., after befing fired by ExOil over a dispute with his boss. ExOil has just discovered that Roger is at SeedGene, and also that SeedGene is now advertising high-oil soybean seeds. ExOil suspects that Roger stole their seeds and gave them to SeedGene to produce their own high oleic acid variety. ExOil wants to test some of the seeds from their competitor to see if they are the same strain in order to support their accusation that SeedGene is violating their patent. The case is designed for use with advanced biology students or introductory genetics students.
Schamber, Elaine M.; Hammond, Paul A.
Effective and efficient rnultiscale modeling is essential to advance both the science and synthesis in a, wide array of fields such as physics, chemistry, materials science; biology, biotechnology and pharmacology. This study investigates the efficacy and potential of rising genetic algorithms for rnultiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry. The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo 1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2--9 orders-of-magnitude increase in real-time dynamics simulations taking 4--7 orders-of-magnitude less CPU time. The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene---two common building blocks in organic chemistry---indicate that MOGAs produce High-quality semiempirical methods that (1) are stable to small perturbations, (2) yield accurate configuration energies on untested and critical excited states, and (3) yield ab initio quality excited-state dynamics. The proposed method enables simulations of more complex systems to realistic, multi-picosecond timescales, well beyond previous attempts or expectation of human experts, and 2--3 orders-of-magnitude reduction in computational cost. While the two applications use simple evolutionary operators, in order to tackle more complex systems, their scalability and limitations have to be investigated. The second part of the thesis addresses some of the challenges involved with a successful design of genetic algorithms and genetic programming for multiscale modeling. The first issue addressed is the scalability of genetic programming, where facetwise models are built to assess the population size required by GP to ensure adequate supply of raw building blocks and also to ensure accurate decision-making between competing building blocks. This study also presents a design of competent genetic programming, where traditional fixed recombination operators are replaced by building and sampling probabilistic models of promising candidate programs. The proposed scalable GP, called extended compact GP (eCGP), combines the ideas from extended compact genetic algorithm (eCGA) and probabilistic incremental program evolution (PIPE) and adaptively identifies, propagates and exchanges important subsolutions of a search problem. Results show that eCGP scales cubically with problem size on both GP-easy and GP-hard problems. Finally, facetwise models are developed to explore limitations of scalability of MOGAs, where the scalability of multiobjective algorithms in reliably maintaining Pareto-optimal solutions is addressed. The results show that even when the building blocks are accurately identified, massive multimodality of the search problems can easily overwhelm the nicher (diversity preserving operator) and l
Sastry, Kumara Narasimha
It is proposed that the primordial genetic material could have been peptide nucleic aicds,i.e., DNA analogues having a peptide backbone. PNA momomers based on the amino acid, ?, ?-diaminobutyric acid or ornithine are suggested as compounds that could have been formed in the prebiotic soup. Finally, the possibility of a PNA/RNA world is presented, in which PNA constitutes the stable genetic material, while RNA which may be polymerized using the PNA as template accounts for enzymatic activities including PNA replication.
Nielsen, Peter Egil
Viral exanthems are mostly associated with self-limited diseases. However, in some cases diagnosis of an exanthem may be crucial to patients and their contacts. Certain exanthems have fairly characteristic morphology, but in many cases an accurate diagnosis cannot be made on the basis of morphology alone. Historical factors may be helpful when evaluating these patients, specifically their disease contacts, immunization record, previous exanthematous illnesses, and associated prodromal symptoms. Some illnesses are seasonal and this knowledge may be useful. This manuscript reviews a number of common childhood exanthems. We included the most common viral exanthems encountered by primary-care physicians and dermatologists. PMID:12952751
Scott, Lycia A; Stone, Mary Seabury
In response to the potential use of viruses as biological weapons, we have established the Viral Biological-threat Bioinformatics Resource (VBBR) that collects, catalogs, annotates, and analyzes genetic information related to potential viral threats. This...
E. J. Lefkowitz
Polyamidoamine (PAMAM) dendrimers have steadily grown in popularity in the past decade in a variety of disciplines, ranging from materials science to biomedicine. This can be attributed in part to their use in applications that range from computer toners to medical diagnostics. PAMAM dendrimers are safe and nonimmunogenic, and can function as highly efficient cationic polymer vectors for delivering genetic
Jonathan D. Eichman; Anna U. Bielinska; Jolanta F. Kukowska-Latallo; James R. Baker
This report addresses special hazards that might arise from the temporary or permanent incorporation of various radionuclides into the genetic material of the cell. Certain radionuclides, principally tritium and krypton, are released from nuclear power plants and fuel reprocessing facilities, and there is public concern about the possible hazards of the build-up of these radionuclides in the biosphere.
Two virus types have been clearly shown to have epidemiologic importance in viral gastroenteritis, i.e., rotavirus and Norwalk virus. Four other virus types have been associated with gastroenteritis but their epidemiologic importance is not yet known, i.e...
N. R. Blacklow G. Cukor
Two virus types have been clearly shown to have epidemiologic importance in viral gastroenteritis, i.e., rotavirus and Norwalk virus. Four other virus types have been associated with gastroenteritis but their epidemiologic importance is not yet known, i.e., enteric adenovirus, ca...
Despite recent progress on nanocatalysis, there exist several critical challenges in simple and readily controllable nanocatalyst synthesis including the unpredictable particle growth, deactivation of catalytic activity, cumbersome catalyst recovery and lack of in-situ reaction monitoring. In this dissertation, two novel approaches are presented for the fabrication of viral-templated palladium (Pd) nanocatalysts, and their catalytic activities for dichromate reduction reaction and Suzuki Coupling reaction were thoroughly studied. In the first approach, viral template based bottom-up assembly is employed for the Pd nanocatalyst synthesis in a chip-based format. Specifically, genetically displayed cysteine residues on each coat protein of Tobacco Mosaic Virus (TMV) templates provide precisely spaced thiol functionalities for readily controllable surface assembly and enhanced formation of catalytically active Pd nanoparticles. Catalysts with the chip-based format allow for simple separation and in-situ monitoring of the reaction extent. Thorough examination of synthesis-structure-activity relationship of Pd nanoparticles formed on surface-assembled viral templates shows that Pd nanoparticle size, catalyst loading density and catalytic activity of viral-templated Pd nanocatalysts can be readily controlled simply by tuning the synthesis conditions. The viral-templated Pd nanocatalysts with optimized synthesis conditions are shown to have higher catalytic activity per unit Pd mass than the commercial Pd/C catalysts. Furthermore, tunable and selective surface assembly of TMV biotemplates is exploited to control the loading density and location of Pd nanocatalysts on solid substrates via preferential electroless deposition. In addition, the catalytic activities of surface-assembled TMV-templated Pd nanocatalysts were also investigated for the ligand-free Suzuki Coupling reaction under mild reaction conditions. The chip-based format enables simple catalyst separation and reuse as well as facile product recovery. Reaction condition studies show that the solvent ratio played an important role in the selectivity of the Suzuki reaction, and that a higher water/acetonitrile ratio significantly facilitated the cross-coupling pathway. Meanwhile, in-depth characterizations including Atomic Force Microscopy (AFM), Grazing Incidence Small Angle X-ray Scattering (GISAXS), Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) and X-ray Photoelectron Spectroscopy (XPS) were carried out for these chip-based viral-templated Pd nanocatalysts. In the second approach, catalytically active TMV-templated Pd nanoparticles are encapsulated in readily exploited polymeric microparticle formats. Specifically, small (1˜2 nm), uniform and highly crystalline palladium (Pd) nanoparticles are spontaneously formed along (TMV) biotemplates without external reducing agents. The as-prepared Pd-TMV complexes are integrated into the hybrid poly(ethylene glycol)(PEG)-based microparticles via replica molding (RM) technique in a simple, robust and highly reproducible manner. The Pd-TMV complex structure was characterized by Transmission Electron Microscopy (TEM). The hybrid Pd-TMV-PEG microparticles are examined to have high catalytic activity, recyclability and stability through dichromate reduction. Combined these findings represent a significant step toward simple, robust, scalable synthesis and fabrication of efficient biotemplate-supported Pd nanocatalysts in readily deployable polymeric formats with high capacity in a well-controlled manner. These two simple, robust and readily controllable approaches for the fabrication of viral-templated Pd nanocatalysts, in both chip-based and hydrogel-encapsulated formats, can be readily extended to a variety of other nano-bio hybrid material synthesis in other catalytic reaction systems.
The triggering cause of keloid formation on a healing wound remains an enigma. In fact, the hypotheses put forward so far to explain this phenomenon seem inconsistent with some clinical features of the disease. The recently established bonds between infectious agents and some pathologies of unknown origin such as peptic ulcer disease, Kaposi's sarcoma or cervical cancer among others led us to consider a potential infectious origin for keloids. This paper presents an infection-based hypothesis (specifically, a viral hypothesis) intended to account for most of their clinical features. Essentially, we hypothesize that healthy individuals carrying a virus, whether known or unknown, associated to some adjuvant, and having some genetic susceptibility, may develop keloids during the scar maturation process in the following manner: the virus would make the bone marrow or lymphatic system its reservoir, residing there in a silent state, and reach the wound via two different mechanisms. The primary mechanism might use an internal circuit through which the viral genome would be transported from its myeloid reservoir to the wound via bone marrow or circulating fibrocytes chemotactically attracted to the damaged skin region. The secondary mechanism might involve an external circuit by which infecting virions via saliva would be shed in the wound directly (preferentially in the sternal or deltoid region) or indirectly (other satellite regions) via the hands or some fomites. A combination of both mechanisms might also be possible. Once in the wound, the virus would switch from a silent state to a latent state by effect of some chemical stimulus probably generated during the tissue repair process; in the new state, the transcription of some of the powerful viral proteins might cause thorough derailment of the normal repair process. As a result, keloid growth might depend both on individual susceptibility and on the viral load deposited into the wound; the greater the susceptibility and viral load were, the more markedly the keloid would develop and the more aggressive it would be. PMID:17509771
Alonso, Pedro E; Rioja, Luis F; Pera, Carlos
The presence of genetically modified organisms (GMOs) in food and feed products is subject to regulation in the European Union (EU) and elsewhere. As part of the EU authorization procedure for GMOs intended for food and feed use, reference materials must be produced for the quality control of measurements to quantify the GMOs. Certified reference materials (CRMs) are available for a range of herbicide- and insect-resistant genetically modified crops such as corn, soybean, and cotton. Here the development of the first CRM for a GMO that differs from its non-GMO counterpart in a major compositional constituent, that is, starch, is described. It is shown that the modification of the starch composition of potato (Solanum tuberosum L.) tubers, together with other characteristics of the delivered materials, have important consequences for the certification strategy. Moreover, the processing and characterization of the EH92-527-1 potato material required both new and modified procedures, different from those used routinely for CRMs produced from genetically modified seeds. PMID:17508757
Broothaerts, Wim; Corbisier, Philippe; Emons, Hendrik; Emteborg, Håkan; Linsinger, Thomas P J; Trapmann, Stefanie
Schizophrenia is a severe neurodevelopmental disorder with genetic and environmental etiologies. Prenatal viral/bacterial infections and inflammation play a major role in the genesis of schizophrenia. In this review, we describe a viral model of schizophrenia tested in mice whereby the offspring of mice prenatally infected with influenza at E7, E9, E16, and E18 show significant gene, protein, and structural abnormalities postnatally. Similarly, we describe data on rodents exposed to bacterial infection or injected with a synthetic viral mimic (PolyI:C) also demonstrating brain structural and behavioral abnormalities. Moreover, human serologic data has been indispensible in supporting the viral theory of schizophrenia. Individuals born seropositive for bacterial and viral agents are at a significantly elevated risk of developing schizophrenia. While the specific mechanisms of prenatal viral/bacterial infections and brain disorder are unclear, recent findings suggest the maternal inflammatory response may be associated with fetal brain injury. Preventive and therapeutic treatment options are also proposed. This review presents data related to epidemiology, human serology, and experimental animal models which support the viral model of schizophrenia.
Kneeland, Rachel E.; Fatemi, S. Hossein
Disease progression in HIV-infected individuals varies greatly, and while the environmental and host factors influencing this variation have been widely investigated, the viral contribution to variation in set-point viral load, a predictor of disease progression, is less clear. Previous studies, using transmission-pairs and analysis of phylogenetic signal in small numbers of individuals, have produced a wide range of viral genetic effect estimates. Here we present a novel application of a population-scale method based in quantitative genetics to estimate the viral genetic effect on set-point viral load in the UK subtype B HIV-1 epidemic, based on a very large data set. Analyzing the initial viral load and associated pol sequence, both taken before anti-retroviral therapy, of 8,483 patients, we estimate the proportion of variance in viral load explained by viral genetic effects to be 5.7% (CI 2.8-8.6%). We also estimated the change in viral load over time due to selection on the virus and environmental effects to be a decline of 0.05 log10 copies/mL/year, in contrast to recent studies which suggested a reported small increase in viral load over the last 20 years might be due to evolutionary changes in the virus. Our results suggest that in the UK epidemic, subtype B has a small but significant viral genetic effect on viral load. By allowing the analysis of large sample sizes, we expect our approach to be applicable to the estimation of the genetic contribution to traits in many organisms. PMID:24789308
Hodcroft, Emma; Hadfield, Jarrod D; Fearnhill, Esther; Phillips, Andrew; Dunn, David; O'Shea, Siobhan; Pillay, Deenan; Leigh Brown, Andrew J
Disease progression in HIV-infected individuals varies greatly, and while the environmental and host factors influencing this variation have been widely investigated, the viral contribution to variation in set-point viral load, a predictor of disease progression, is less clear. Previous studies, using transmission-pairs and analysis of phylogenetic signal in small numbers of individuals, have produced a wide range of viral genetic effect estimates. Here we present a novel application of a population-scale method based in quantitative genetics to estimate the viral genetic effect on set-point viral load in the UK subtype B HIV-1 epidemic, based on a very large data set. Analyzing the initial viral load and associated pol sequence, both taken before anti-retroviral therapy, of 8,483 patients, we estimate the proportion of variance in viral load explained by viral genetic effects to be 5.7% (CI 2.8–8.6%). We also estimated the change in viral load over time due to selection on the virus and environmental effects to be a decline of 0.05 log10 copies/mL/year, in contrast to recent studies which suggested a reported small increase in viral load over the last 20 years might be due to evolutionary changes in the virus. Our results suggest that in the UK epidemic, subtype B has a small but significant viral genetic effect on viral load. By allowing the analysis of large sample sizes, we expect our approach to be applicable to the estimation of the genetic contribution to traits in many organisms.
Hodcroft, Emma; Hadfield, Jarrod D.; Fearnhill, Esther; Phillips, Andrew; Dunn, David; O'Shea, Siobhan; Pillay, Deenan; Leigh Brown, Andrew J.
Information on psoriasis among parents and siblings in 14,008 families has been collected. On the basis of this material, evidence for monogenetic autosomal recessive inheritance of psoriasis has recently been presented. Indications from more than one type of non-pustular psoriasis has been obtained from the population genetic data. Molecular genetic linkage analysis of psoriasis to a number of polymorphic genetic markers for a large number of families has been made. It is apparent that there is genetic heterogeneity in a psoriasis population with regard to psoriasis genes. Using the computer program Linkage 5.0 and a formula for heterogeneity, a lodscore over 3.0 for one locus has been obtained. This locus has further been confirmed by several other markers in the vicinity. The locus found is linked to slightly over half of the families, indicating that there are more genetically independent types of psoriasis. The age at onset of those families that are apparently linked to this locus have a slightly higher age at onset than those not linked to that locus but with a considerable overlap. In spite of close coverage of the whole chromosomes number 6 and 17, no linkage has been found in this regions. This indicates that neither the HLA region nor the region earlier found to be involved in one family with psoriasis are primarily involved in our families.
Wahlstroem, J.; Swanbeck, G.; Inerot, A. [ Univ. of Goeteborg (Sweden)] [and others
In recent years, the development of powerful viral gene transfer techniques has greatly facilitated the study of gene function. This review summarises some of the viral delivery systems routinely used to mediate gene transfer into cell lines, primary cell cultures and in whole animal models. The systems described were originally discussed at a 1-day European Tissue Culture Society (ETCS-UK) workshop that was held at University College London on 1st April 2009. Recombinant-deficient viral vectors (viruses that are no longer able to replicate) are used to transduce dividing and post-mitotic cells, and they have been optimised to mediate regulatable, powerful, long-term and cell-specific expression. Hence, viral systems have become very widely used, especially in the field of neurobiology. This review introduces the main categories of viral vectors, focusing on their initial development and highlighting modifications and improvements made since their introduction. In particular, the use of specific promoters to restrict expression, translational enhancers and regulatory elements to boost expression from a single virion and the development of regulatable systems is described. PMID:19830583
Howarth, Joanna L; Lee, Youn Bok; Uney, James B
Although rubella is the only virus which can be regarded in the strict sense of the term a teratogen, there is no convincing evidence that other viruses can cause fetal damage of varying severity. The risk to the fetus appears to depend on the nature of the infectious agent, the maternal immune status and the gestational age when infection takes place. The possibility that subclinical maternal infections may cause damage must not be overlooked. As some of the viruses referred to can cause damage after the period of organogenesis, the use of the term 'teratogenic efect' in relation to viral infections is considered to be inappropriate. PMID:184117
Dudgeon, J A
It has been hypothesized that a single mutation at a highly conserved amino acid site (HCS) can be severely deleterious to HIV in most if not all isolate-specific genetic backgrounds. Consequently, potentially universal HIV-1 vaccines exclusively targeting highly conserved regions of the viral proteome have been proposed. To test this hypothesis, we examined the impact of 10 Gag-p24 and 9 Env-gp120 HCS single mutations on viral fitness. In the original founder sequence of the subject in whom these mutations were identified, all Gag-p24 HCS mutations significantly reduced viral replication fitness, including 7 that were lethal. Similar results were obtained at 9/10 sites when the same mutations were introduced into the founder sequences of two epidemiologically unlinked subjects. In contrast, none of the 9 Env-gp120 HCS mutations were lethal in the original founder sequence, and four had no fitness cost. Hence, HCS mutations in Gag-p24 are likely to be severely deleterious in different HIV-1 subtype B backgrounds; however, some HCS mutations in both Gag-p24 and Env-gp120 fragments can be well tolerated. Therefore, when designing HIV-1 immunogens that are intended to force the virus to nonviable escape pathways, the fitness constraints on the HIV segments included should be considered beyond their conservation level. PMID:24713822
Liu, Yi; Rao, Ushnal; McClure, Jan; Konopa, Philip; Manocheewa, Siriphan; Kim, Moon; Chen, Lennie; Troyer, Ryan M; Tebit, Denis M; Holte, Sarah; Arts, Eric J; Mullins, James I
In the present study, 122 maize local cultivars and adapted exotic germplasm from Thailand were used to develop open pollinate varieties (OPVs) using modified ear-to-row scheme, top-cross or test-cross programmes. Ten new maize OPVs with distinct characters were created based on the precise breeding objectives and directional design. The selection of breeding materials was based upon three factors: elite performance, broad adaptability, and genetic diversity. The synthesizing system provided four features: genetic mixing and recombination, equal comparable genetic contribution, mild selection pressure, and maximum intermating for genetic equilibrium (i.e., the female traits were close for the genetic com-positions). Subsequently, Suwan 1 composite and its deritives (Suwan 2, Suwan 3 composite, Suwan 5 and KS24 synthetics), KS6 and KS28 synthetics with the dent type of different origins, and Caripeno DMR composite, KS23, and KS27 synthetics with the dent type of Non-Suwan 1 origin were developed. These OPVs had been improved for 2~13 cycles using S1 recurrent selection method. About 50 inbred lines were developed from these OPVs, and 16 elite single (three-way) crosses were combined and released from these inbred lines. At present, at least one parental inbred line of all the tropical hybrids was derived from Suwan (KS) germplasm in Thailand. Based on the theory of the synthesizing OPVs and developing inbred lines, this paper discussed the genetic moderate diversity, relationship, heterotic group, and patterns for synthesizing OPVs, and inspiration for composed OPVs to heterosis breeding. PMID:22207385
Sansern, Jampatong; Chaba, Jampatong
Students learn how viruses invade host cells and hijack the hosts' cell-reproduction mechanisms in order to make new viruses, which can in turn attack additional host cells. Students also learn how the immune system responds to a viral invasion, eventually defeating the virusesâif all goes well. Finally, they consider the special case of HIV, in which the virus' host cell is a key component of the immune system itself, severely crippling it and ultimately leading to AIDS. The associated activity sets the stage for this lesson with a dramatic simulation that allows students to see for themselves how quickly a virus can spread through a population, and then challenges students to determine who the initial bearers of the virus were.
Engineering K-Phd Program
This report presents the interim results of the genetic and animal toxicity testing program; of SRC-I products, process intermediates, and waste materials. It also discusses the structure of the program, including the philosophy underlying its design, as ...
B. Z. Drozdowicz C. M. Kelly
This Genetics activity helps students to understand the basic principles of genetics, including concepts of recessive and dominant alleles, relationships of phenotype to genotype, Punnett squares, and pedigree analysis. The introductory section on inheritance of albinism demonstrates how understanding meiosis and fertilization provides the basis for understanding inheritance and Punnett squares. The next two sections, Coin Toss Genetics and analysis of class data on the sex makeup of sibships, help students understand the probabilistic nature of Punnett square predictions. The final activities analyze the genetics of sickle cell anemia and pedigrees for families with albinism and achondroplasia.
Doherty, Jennifer; Waldron, Ingrid; Poethig, Scott
Traditional approach of inactivated or live-attenuated vaccine immunization has resulted in impressive success in the reduction and control of infectious disease outbreaks. However, many pathogens remain less amenable to deal with the traditional vaccine strategies, and more appropriate vaccine strategy is in need. Recent discoveries that led to increased understanding of viral molecular biology and genetics has rendered the used of viruses as vaccine platforms and as potential anti-cancer agents. Due to their ability to effectively induce both humoral and cell-mediated immune responses, viral vectors are deemed as an attractive alternative to the traditional platforms to deliver vaccine antigens as well as to specifically target and kill tumor cells. With potential targets ranging from cancers to a vast number of infectious diseases, the benefits resulting from successful application of viral vectors to prevent and treat human diseases can be immense.
Traditional approach of inactivated or live-attenuated vaccine immunization has resulted in impressive success in the reduction and control of infectious disease outbreaks. However, many pathogens remain less amenable to deal with the traditional vaccine strategies, and more appropriate vaccine strategy is in need. Recent discoveries that led to increased understanding of viral molecular biology and genetics has rendered the used of viruses as vaccine platforms and as potential anti-cancer agents. Due to their ability to effectively induce both humoral and cell-mediated immune responses, viral vectors are deemed as an attractive alternative to the traditional platforms to deliver vaccine antigens as well as to specifically target and kill tumor cells. With potential targets ranging from cancers to a vast number of infectious diseases, the benefits resulting from successful application of viral vectors to prevent and treat human diseases can be immense. PMID:23858400
Choi, Youngjoo; Chang, Jun
Polyamidoamine (PAMAM) dendrimers have steadily grown in popularity in the past decade in a variety of disciplines, ranging from materials science to biomedicine. This can be attributed in part to their use in applications that range from computer toners to medical diagnostics. PAMAM dendrimers are safe and nonimmunogenic, and can function as highly efficient cationic polymer vectors for delivering genetic material into cells. They have been shown to be as efficient or more efficient than either cationic liposomes or other cationic polymers (e.g. polyethylenimine, polylysine) for in vitro gene transfer. This article will focus on the application of PAMAM dendrimers as a nonviral gene delivery vector from the initial discovery of this capacity to the most recent experimental findings. PMID:10884679
Eichman; Bielinska; Kukowska-Latallo; Baker
This synopsis reviews published in vivo studies on possible health consequences of genetically modified food and feed where the ingredients in question have consisted of genetically modified plant materials. The following, however, have not been taken into consideration:--ingredients consisting of genetically modified microorganisms or parts of animals/fish--ingredients produced by/from genetically modified organisms but without any DNA present--studies on consequences for the environment or biodiversity--in vitro studies or computer simulations. According to a Norwegian report "Gen-mat" (NOU 2000:29), and a more recent search in Medline and Citations Index, to our knowledge a total of ten studies have been published on the health effects of GM-foods and feeds. In this minireview the data made available in these published studies is discussed. PMID:12803276
Pryme, Ian F; Lembcke, Rolf
There are many viruses whose genetic material is protected by a closed elongated protein shell. Unlike spherical viruses, the structure and construction principles of these elongated capsids are not fully known. In this article, we have developed a general geometrical model to describe the structure of prolate or bacilliform capsids. We show that only a limited set of tubular architectures can be built closed by hemispherical icosahedral caps. In particular, the length and number of proteins adopt a very special set of discrete values dictated by the axial symmetry (fivefold, threefold, or twofold) and the triangulation number of the caps. The results are supported by experimental observations and simulations of simplified physical models. This work brings about a general classification of elongated viruses that will help to predict their structure, and to design viral cages with tailored geometrical properties for biomedical and nanotechnological applications. PMID:20550912
Luque, Antoni; Reguera, David
Peritoneal dissemination is a common and fatal clinical manifestation of gastric cancer with few effective therapies available.\\u000a Natural Newcastle disease virus (NDV) has been shown to be an effective oncolytic agent, and recent advances now allow genetic\\u000a manipulation of this virus to improve cancer killing and safety. This study was designed to investigate the effectiveness\\u000a of a genetically engineered NDV
Kyo Young Song; Joyce Wong; Lorena Gonzalez; Gang Sheng; Dmitriy Zamarin; Yuman Fong
Summary Advances in understanding and controlling genes and their expression have set the stage to alter genetic material to fight or prevent disease with brain tumors being among one of the first human malignancies to be targeted by gene therapy. All proteins are coded for by DNA and most neoplastic diseases ultimately result from the expression or lack thereof with one or more proteins (e.g., coded by oncogenes or tumor suppressor genes, respectively). In theory, therefore, diseases could be treated by expression of the appropriate protein in the affected cells. Gene therapy is an experimental treatment that involves introducing genetic material (DNA or RNA) into cells, and it has made important advances in the past decade. Within this short time span, it has moved from the conceptual laboratory research stage to clinical translational trials for brain tumors. The most efficient approaches for gene delivery are based on viral vectors, which have been proven relatively safe in the CNS, despite occasional cases of morbidity and death in non-neurosurgical trials. However, the human response to various viral vectors can not be predicted in a reliable manner from animal experimentation, nor can size, consistency, and extent of experimental brain tumors in mouse models reflect the large, necrotic, infiltrative nature of malignant gliomas. Furthermore, the problem of delivering genetic vectors into solid brain tumors and the efficiency in situ gene transfer remains one of the most significant hurdles in gene therapy.
Asadi-Moghaddam, Kaveh; Chiocca, E. Antonio
This report presents the interim results of the genetic and animal toxicity testing program; of SRC-I products, process intermediates, and waste materials. It also discusses the structure of the program, including the philosophy underlying its design, as well as the sources, processing, and sample handling of the materials tested. Finally, it summarizes the results of the tests completed at the
B. Z. Drozdowicz; C. M. Kelly
The compartmentalization of viral variants in distinct host tissues is a frequent event in many viral infections. Although hepatitis B virus (HBV) classically is considered hepatotropic, it has strong lymphotropic properties as well. However, unlike other viruses, molecular evolutionary studies to characterize HBV variants in compartments other than hepatocytes or sera have not been performed. The present work attempted to characterize HBV sequences from the peripheral blood leukocytes (PBL) of a large set of subjects, using advanced molecular biology and computational methods. The results of this study revealed the exclusive compartmentalization of HBV subgenotype Ae/A2-specific sequences with a potent immune escape G145R mutation in the PBL of the majority of the subjects. Interestingly, entirely different HBV genotypes/subgenotypes (C, D, or Aa/A1) were found to predominate in the sera of the same study populations. These results suggest that subgenotype Ae/A2 is selectively archived in the PBL, and the high prevalence of G145R indicates high immune pressure and high evolutionary rates of HBV DNA in the PBL. The results are analogous to available literature on the compartmentalization of other viruses. The present work thus provides evidence in favor of the compartment-specific abundance, evolution, and emergence of the potent immune escape mutant. These findings have important implications in the field of HBV molecular epidemiology, transmission, transfusion medicine, organ transplantation, and vaccination strategies.
Datta, Sibnarayan; Panigrahi, Rajesh; Biswas, Avik; Chandra, Partha K.; Banerjee, Arup; Mahapatra, Pradip K.; Panda, Chinmoy K.; Chakrabarti, Shekhar; Bhattacharya, Sujit K.; Biswas, Kuntal; Chakravarty, Runu
A novel, real-valued Genetic Algorithm (GA) was designed and implemented to minimize the reflectivity and/or transmissivity of an arbitrary number of homogeneous, lossy dielectric or magnetic layers of arbitrary thickness positioned at either the center of an infinitely long rectangular waveguide, or adjacent to the perfectly conducting backplate of a semi-infinite, shorted-out rectangular waveguide. Evolutionary processes extract the optimal physioelectric constants falling within specified constraints which minimize reflection and/or transmission over the frequency band of interest. This GA extracted the unphysical dielectric and magnetic constants of three layers of fictitious material placed adjacent to the conducting backplate of a shorted-out waveguide such that the reflectivity of the configuration was 55 dB or less over the entire X-band. Examples of the optimization of realistic multi-layer absorbers are also presented. Although typical Genetic Algorithms require populations of many thousands in order to function properly and obtain correct results, verified correct results were obtained for all test cases using this GA with a population of only four.
Hall, John Michael
Gene therapy is a promising therapeutic modality for the treatment of genetic disorders. Gene therapy has been able to correct many of the genetic diseases at the root of their cause by systematizing genetic information that encodes for all functions of every cell in our body. Recent studies have identified novel molecular targets for genetic disorders that can be used to deliver gene to the specific site. Gene therapy applications require safe and efficient method for gene transfer. Over the last decade, non-viral and viral gene therapy approaches have been tested in preclinical studies and human clinical trials. Gene delivery via conventional means by using viral vectors has several undesirable side effects such as insertion of mutational viral gene into the host genome and overwhelming immune and inflammatory responses. As compared to viral vectors, non-viral vehicles has received great attention due to their several favorable properties, including low toxicity and immunogenicty, resistance to nuclease, and their high affinity for DNA targets. Here, we describe how non-viral gene-transfer vehicles have been used and can be modified to target specific tissues for gene therapy. This review focuses on existing and emerging patents on non-viral based genetic engineering strategies for the delivery of therapeutic molecules or several approaches for genetic disorder treatment. PMID:19075945
Goyal, Amit K; Khatri, Kapil; Vyas, Suresh P
learning about our genetic make up We've been learning about DNA. Go to each web site, read and follow the instructions of the activities provided. On a piece of paper write your answers to the following questions and submit your work. Put the site for each of the questions you are answering. The first site is, ...
Many recessive genetic disorders are found at a higher incidence in people of Ashkenazi Jewish (AJ) descent than in the general population. The American College of Medical Genetics and the American College of Obstetricians and Gynecologists have recommended that individuals of AJ descent undergo carrier screening for Tay Sachs disease, Canavan disease, familial dysautonomia, mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia type C, Bloom syndrome, and Gaucher disease. Although these recommendations have led to increased test volumes and number of laboratories offering AJ screening, well-characterized genomic reference materials are not publicly available. The Centers for Disease Control and Prevention-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the genetic testing community and Coriell Cell Repositories, have developed a panel of characterized genomic reference materials for AJ genetic testing. DNA from 31 cell lines, representing many of the common alleles for Tay Sachs disease, Canavan disease, familial dysautonomia, mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia type C, Bloom syndrome, Gaucher disease, and glycogen storage disease, was prepared by the Repository and tested in six clinical laboratories using three different PCR-based assay platforms. A total of 33 disease alleles was assayed and 25 different alleles were identified. These characterized materials are publicly available from Coriell and may be used for quality control, proficiency testing, test development, and research. PMID:19815695
Kalman, Lisa; Wilson, Jean Amos; Buller, Arlene; Dixon, John; Edelmann, Lisa; Geller, Louis; Highsmith, William Edward; Holtegaard, Leonard; Kornreich, Ruth; Rohlfs, Elizabeth M; Payeur, Toby L; Sellers, Tina; Toji, Lorraine; Muralidharan, Kasinathan
Hepatitis B virus (HBV) is a major etiological factor associated with hepatocarcinogenesis, but its role in the transformation process remains unclear. We previously documented the accumulation of genetic alterations in a HBV-transfected cell line. In the present study, we addressed the effect of HBV and its replication on the genome and phenotype of the host cell. Parental HBV-free Hep G2
Kristin W Livezey; Dmitri Negorev; Daniela Simon
Abstract Genetic and environmental factors are involved in the pathogenesis of non-Hodgkin lymphoma (NHL). The present study aimed to investigate the association between cytotoxic T-lymphocyte antigen 4 (CTLA-4) genetic polymorphism, hepatitis C virus (HCV) infection and B-cell NHL risk in Egypt. Genotyping of CTLA-4 single nucleotide polymorphisms (SNPs) was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay for 181 adult patients with B-NHL and 200 controls. Our study revealed that CTLA-4 + 49 A/G polymorphism conferred increased risk of B-NHL (odds ratio [OR] = 1.7, 95% confidence interval [CI] = 1.36-2.565). The prevalence of HCV infection in individuals harboring the mutant genotype + 49 A/G and - 318 C/T SNPs was higher in patients with B-NHL and was associated with increased risk of B-NHL (OR = 2.79, 95% CI = 1.24-6.93 for + 49 A/G and OR = 3.9, 95% CI = 1.01-15.98 for - 318 C/T). In conclusion, some SNPs of CTLA-4 are genetic risk factors for B-NHL. Moreover, this study identified an association of CTLA-4 + 49 A/G and - 318 C/T promoter polymorphisms with HCV infection. PMID:23829277
Khorshied, Mervat Mamdooh; Gouda, Heba Mahmoud; Khorshid, Ola M Reda
Verification of genetic programming (GP) as a new approach for solving inverse problems of moisture transport in building materials is presented. The GP is applied on experimental data in order to optimize the moisture diffusivity as a function of moisture content. The results show that GP is very powerful tool for the inverse analysis of transport equations.
Ko?í, Jan; Mad?ra, Ji?í; ?erný, Robert
Myotonic dystrophy type 1 (DM1) is caused by expansion of a CTG triplet repeat in the 3' untranslated region of the DMPK gene that encodes a serine-threonine kinase. Patients with larger repeats tend to have a more severe phenotype. Clinical laboratories require reference and quality control materials for DM1 diagnostic and carrier genetic testing. Well-characterized reference materials are not available. To address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the genetic testing community, the National Registry of Myotonic Dystrophy and Facioscapulohumeral Muscular Dystrophy Patients and Family Members, and the Coriell Cell Repositories, has established and characterized cell lines from patients with DM1 to create a reference material panel. The CTG repeats in genomic DNA samples from 10 DM1 cell lines were characterized in three clinical genetic testing laboratories using PCR and Southern blot analysis. DMPK alleles in the samples cover four of five DM1 clinical categories: normal (5 to 34 repeats), mild (50 to 100 repeats), classical (101 to 1000 repeats), and congenital (>1000 repeats). We did not identify or establish Coriell cell lines in the premutation range (35 to 49 repeats). These samples are publicly available for quality control, proficiency testing, test development, and research and should help improve the accuracy of DM1 testing. PMID:23680132
Kalman, Lisa; Tarleton, Jack; Hitch, Monica; Hegde, Madhuri; Hjelm, Nick; Berry-Kravis, Elizabeth; Zhou, Lili; Hilbert, James E; Luebbe, Elizabeth A; Moxley, Richard T; Toji, Lorraine
Myotonic dystrophy type 1 (DM1) is caused by expansion of a CTG triplet repeat in the 3? untranslated region of the DMPK gene that encodes a serine-threonine kinase. Patients with larger repeats tend to have a more severe phenotype. Clinical laboratories require reference and quality control materials for DM1 diagnostic and carrier genetic testing. Well-characterized reference materials are not available. To address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the genetic testing community, the National Registry of Myotonic Dystrophy and Facioscapulohumeral Muscular Dystrophy Patients and Family Members, and the Coriell Cell Repositories, has established and characterized cell lines from patients with DM1 to create a reference material panel. The CTG repeats in genomic DNA samples from 10 DM1 cell lines were characterized in three clinical genetic testing laboratories using PCR and Southern blot analysis. DMPK alleles in the samples cover four of five DM1 clinical categories: normal (5 to 34 repeats), mild (50 to 100 repeats), classical (101 to 1000 repeats), and congenital (>1000 repeats). We did not identify or establish Coriell cell lines in the premutation range (35 to 49 repeats). These samples are publicly available for quality control, proficiency testing, test development, and research and should help improve the accuracy of DM1 testing.
Kalman, Lisa; Tarleton, Jack; Hitch, Monica; Hegde, Madhuri; Hjelm, Nick; Berry-Kravis, Elizabeth; Zhou, Lili; Hilbert, James E.; Luebbe, Elizabeth A.; Moxley, Richard T.; Toji, Lorraine
A genetic algorithm (GA)-inspired method to effectively map out low-energy configurations of doped metal oxide materials is presented. Specialized mating and mutation operations that do not alter the identity of the parent metal oxide have been incorporated to efficiently sample the metal dopant and oxygen vacancy sites. The search algorithms have been tested on lanthanide-doped ceria (L=Sm,Gd,Lu) with various dopant concentrations. Using both classical and first-principles density-functional-theory (DFT) potentials, we have shown the methodology reproduces the results of recent systematic searches of doped ceria at low concentrations (3.2% L2O3 ) and identifies low-energy structures of concentrated samarium-doped ceria (3.8% and 6.6% L2O3 ) which relate to the experimental and theoretical findings published thus far. We introduce a tandem classical/DFT GA algorithm in which an inexpensive classical potential is first used to generate a fit gene pool of structures to enhance the overall efficiency of the computationally demanding DFT-based GA search.
Hooper, James; Ismail, Arif; Giorgi, Javier B.; Woo, Tom K.
Subtype C human immunodeficiency virus type 1 (HIV-1C) continues to cause the majority of new cases of mother-to-child transmission (MTCT), and yet there are limited data on HIV-1C transmission. We amplified env from plasma RNA for 19 HIV-1C MTCT pairs, 10 transmitting in utero (IU) and 9 transmitting intrapartum (IP). There was a strong genetic bottleneck between all mother-infant pairs, with a majority of transmission events involving the transmission of a single virus. env genes of viruses transmitted to infants IP, but not IU, encoded Env proteins that were shorter and had fewer putative N-linked glycosylation sites in the V1-V5 region than matched maternal sequences. Viruses pseudotyped with env clones representative of each maternal and infant population were tested for neutralization sensitivity. The 50% inhibitory concentration of autologous serum was similar against both transmitted (infant) and nontransmitted (maternal) viruses in a paired analysis. Mother and infant Env proteins were also similar in sensitivity to soluble CD4, to a panel of monoclonal antibodies, and to heterologous HIV-1C sera. In addition, there was no difference in the breadth or potency of neutralizing antibodies between sera from 50 nontransmitting and 23 IU and 23 IP transmitting HIV-1C-infected women against four Env proteins from heterologous viruses. Thus, while a strong genetic bottleneck was detected during MCTC, with viruses of shorter and fewer glycosylation sites in env present in IP transmission, our data do not support this bottleneck being driven by selective resistance to antibodies.
Russell, Elizabeth S.; Kwiek, Jesse J.; Keys, Jessica; Barton, Kirston; Mwapasa, Victor; Montefiori, David C.; Meshnick, Steven R.; Swanstrom, Ronald
Subtype C human immunodeficiency virus type 1 (HIV-1C) continues to cause the majority of new cases of mother-to-child transmission (MTCT), and yet there are limited data on HIV-1C transmission. We amplified env from plasma RNA for 19 HIV-1C MTCT pairs, 10 transmitting in utero (IU) and 9 transmitting intrapartum (IP). There was a strong genetic bottleneck between all mother-infant pairs, with a majority of transmission events involving the transmission of a single virus. env genes of viruses transmitted to infants IP, but not IU, encoded Env proteins that were shorter and had fewer putative N-linked glycosylation sites in the V1-V5 region than matched maternal sequences. Viruses pseudotyped with env clones representative of each maternal and infant population were tested for neutralization sensitivity. The 50% inhibitory concentration of autologous serum was similar against both transmitted (infant) and nontransmitted (maternal) viruses in a paired analysis. Mother and infant Env proteins were also similar in sensitivity to soluble CD4, to a panel of monoclonal antibodies, and to heterologous HIV-1C sera. In addition, there was no difference in the breadth or potency of neutralizing antibodies between sera from 50 nontransmitting and 23 IU and 23 IP transmitting HIV-1C-infected women against four Env proteins from heterologous viruses. Thus, while a strong genetic bottleneck was detected during MCTC, with viruses of shorter and fewer glycosylation sites in env present in IP transmission, our data do not support this bottleneck being driven by selective resistance to antibodies. PMID:21593171
Russell, Elizabeth S; Kwiek, Jesse J; Keys, Jessica; Barton, Kirston; Mwapasa, Victor; Montefiori, David C; Meshnick, Steven R; Swanstrom, Ronald
Patients with severe viral infections are often not thoroughly evaluated for immunodeficiencies. In this review, we summarize primary immunodeficiencies that predispose individuals to severe viral infections. Some immunodeficiencies enhance susceptibility to disease with a specific virus or family of viruses, whereas others predispose to diseases with multiple viruses in addition to disease with other microbes. Although the role of cytotoxic T cells in controlling viral infections is well known, a number of immunodeficiencies that predispose to severe viral diseases have recently been ascribed to defects in the Toll-like receptor–interferon signaling pathway. These immunodeficiencies are rare, but it is important to identify them both for prognostic information and for genetic counseling. Undoubtedly, additional mutations in proteins in the innate and adaptive arms of the immune system will be identified in the future, which will reveal the importance of these proteins in controlling infections caused by viruses and other pathogens.
Cohen, Jeffrey I.
The potential benefits of gene therapy for neurological diseases such as Parkinson’s, Amyotrophic Lateral Sclerosis (ALS), Epilepsy, and Alzheimer’s are enormous. Even a delay in the onset of severe symptoms would be invaluable to patients suffering from these and other diseases. Significant effort has been placed in developing vectors capable of delivering therapeutic genes to the CNS in order to treat neurological disorders. At the forefront of potential vectors, viral systems have evolved to efficiently deliver their genetic material to a cell. The biology of different viruses offers unique solutions to the challenges of gene therapy, such as cell targeting, transgene expression and vector production. It is important to consider the natural biology of a vector when deciding whether it will be the most effective for a specific therapeutic function. In this review, we outline desired features of the ideal vector for gene delivery to the CNS and discuss how well available viral vectors compare to this model. Adeno-associated virus, retrovirus, adenovirus and herpesvirus vectors are covered. Focus is placed on features of the natural biology that have made these viruses effective tools for gene delivery with emphasis on their application in the CNS. Our goal is to provide insight into features of the optimal vector and which viral vectors can provide these features.
Lentz, Thomas B.; Gray, Steven J.; Samulski, R. Jude
An algorithm combined with back propagation neural network (BPNN) and genetic algorithm (GA) was used in the optimum design of the compositions of an advanced ZrO2/TiB2/Al2O3 nano-micro-composite ceramic tool and die materials. GA was used to fully optimize the network topology, thresholds, and initial connection weights of BPNN. The input parameters are the contents of each compositions of ceramic tool and die materials and the output parameters are mechanical properties including hardness, flexural strength, and fracture toughness. The compositions with optimum mechanical properties can be chosen for materials preparation with less error and the result can be used to guide the experimental process. As a result, the nano-micro-composite ceramic tool and die material with good mechanical properties was then fabricated. It indicated that the algorithm can offer a robust and efficient way for the compositional design of ceramic tool and die materials.
Zhang, Jingjie; Xu, Chonghai; Yi, Mingdong; Fang, Bin
The purpose of this study was to test the hypothesis that genetic variants of estrogen receptor ? (ER?) are associated with the outcomes of hepatitis C virus (HCV) infection. We genotyped the seven single nucleotide polymorphisms (SNPs) (rs2077647, rs9340799, rs2234693, rs1801132, rs9322354, rs2228480 and rs3798577) of ER? and conducted a case-control study in a high-risk Chinese population, including 429 HCV spontaneous clearance cases, 880 persistent infection cases and 1,174 uninfected controls. The C allele of rs2234693 was significantly associated with increased susceptibility to HCV infection [dominant model: adjusted odds ratio (OR)?=?1.377, 95 % confidence interval (CI) =1.126-1.778], and the risk effect remained significant among the younger (?55 years) and hemodialysis subjects (all P?0.007). The other three SNPs variant genotypes also showed significant correlation with elevated risk of HCV infection in different strata (rs2077647 in males; rs9340799 in blood donors; rs1801132 in younger subjects; all P?0.007). It was also discovered that carriage of rs2228480 A allele was more prone to develop persistent HCV infection (dominant model: adjusted OR?=?1.203, 95 % CI?=?1.154-1.552), and the risk effect was more evident in females and blood donors (all P?0.007). Haplotype analyses (rs2077647, rs9340799 and rs2234693) showed that, compared with the most frequent haplotype TAT, CAC played a risk effect in subgroups of younger (P?=?3.24?×?10(-3)) and male (P?=?5.51?×?10(-4)), whereas CAT expressed a protective effect in females (P?=?2.27?×?10(-4)) for HCV infection susceptibility. We first report that these SNPs (rs2077647, rs9340799, rs2234693, rs1801132 and rs2228480) in ER? can influence the outcomes of HCV infection in a high-risk Chinese population. PMID:24395301
Tang, Shaidi; Yue, Ming; Wang, Jiajia; Su, Jing; Yu, Rongbin; Zhou, Donghui; Xu, Ke; Cai, Li; Zhang, Yun; Wang, Jie
The ability to measure HIV-1 viral load has revolutionized our ability to track HIV infection and viral replication. The advent\\u000a of viral load assays has been both a technologic and pragmatic feat, supplying a sturdy clinical measure to guide clinical\\u000a AIDS management. Formerly, clinicians and scientists relied on difficult and cumbersome plasma and peripheral blood mononuclear\\u000a cell cultures for virus
Phyllis J. Kanki; Indu Mani
Gerade in Zeiten zunehmender Reizüberflutung und steigender Reaktanz gegenüber traditionellen Werbeformen gewinnen innovative\\u000a Marketinginstrumente, wie Mobile Viral Marketing, verstärkt an Bedeutung. Ziel des vorliegenden Beitrages ist es, den State\\u000a of the Art des Mobile Viral Marketing zu analysieren. Der Beitrag stellt zunächst Mobile Viral Marketing in Form eines strukturellen\\u000a Beschreibungsmodells unter Verwendung der morphologischen Methode vor. Anschließend werden der Stand
K. Pousttchi; K. Turowski; D. G. Wiedemann
Exogenous cannabinoids or receptor antagonists may influence many cellular and systemic host responses. The anti-inflammatory activity of cannabinoids may compromise host inflammatory responses to acute viral infections, but may be beneficial in persistent infections. In neurons, where innate antiviral/pro-resolution responses include the activation of NOS-1, inhibition of Ca2+ activity by cannabinoids, increased viral replication and disease. This review examines the effect(s) of cannabinoids and their antagonists in viral infections.
Reiss, Carol Shoshkes
The identification of genetically modified (GM) organisms (GMOs) in unknown samples by polymerase chain reaction (PCR) requires\\u000a the use of a positive control sample, containing the target sequence derived from the respective GMO. For this purpose, either\\u000a DNA extracted from suitable reference material or plasmids bearing the sequence are used. In the case of isolated genomic\\u000a DNA, the preparation is
Lillian Roth; Jutta Zagon; Ines Laube; Arne Holst-Jensen; Hermann Broll
An introduction of genetic material from rye, Aegilops and Elymus into durum and common wheat by crossing the wheat species\\u000a with different amphiploids, has been attempted. Meiotic studies of the hybrids demonstrated that the wheat Elymus sibiricus\\u000a amphiploid contained several (two or three) genes suppressing the activity of the wheat homoeologous pairing control system.\\u000a Somatic chromosome studies of the hybrids
V. K. Simonenko; I. I. Motsny; A. L. Sechnyak; M. P. Kulbida
Transplantation of pigment epithelial cells in patients with age-related macular degeneration and Parkinson's disease has the potential to improve functional rehabilitation. Genetic modification of cells before transplantation may allow the delivery of neuroprotective factors to achieve functional improvement. As transplantation of cells modified using viral vectors is complicated by the possible dissemination of viral particles and severe immune reactions, we have explored non-viral methods to insert genetic material in pigment epithelial cells. Using lipofection or nucleofection ARPE-19 cells, freshly isolated and primary retinal and iris pigment epithelial (IPE) cells were transfected with plasmids encoding green fluorescent protein (GFP) and with three plasmids encoding recombinant pigment epithelium-derived factor (PEDF) and GFP. Transfection efficiency was evaluated by fluorescence microscopy and stability of protein expression by immunoblotting. Pigment epithelial cells were successfully transfected with plasmid encoding GFP. Expression of GFP in ARPE-19 was transient, but was observed for up to 1 year in IPE cells. Analysis of pigment epithelial cells transfected with PEDF plasmids revealed that PEDF fusion proteins were successfully expressed and functionally active. In conclusion, efficient transfer of genetic information in pigment epithelial cells can be achieved using non-viral transfection protocols. PMID:19741732
Thumann, G; Stöcker, M; Maltusch, C; Salz, A K; Barth, S; Walter, P; Johnen, S
In this work we genetically programmed the M13 virus, so that the new clone expressed multifunctional coat protein sequences that selectively bind to designated surfaces and species. Using these new clones, composite network consisting of ironphosphate na...
A. Xu D. Oh H. Yi J. Qi K. Xu
An online survey was conducted by the International Life Sciences Institute, Food Biotechnology Committee, on the use of qualitative and quantitative polymerase chain reaction (PCR) assays for cauliflower mosaic virus 35S promoter and Agrobacterium tumefaciens Tnos DNA sequence elements for the detection of genetically engineered (GE) crop plant material. Forty-four testing laboratories around the world completed the survey. The results showed the widespread use of such methods, the multiplicity of published and in-house methods, and the variety of reference materials and calibrants in use. There was an interest on the part of respondents in validated quantitative assays relevant to all GE events that contain these two genetic elements. Data are presented by testing two variations each of five published real-time quantitative PCR methods for 35S detection on eight maize reference materials. The results showed that two of the five methods were not suitable for all the eight reference materials, with poor linear regression parameters and multiple PCR amplification products for some of the reference materials. This study demonstrates that not all 35S methods produce satisfactory results, emphasizing the need for method validation. PMID:19856176
Holden, Marcia J; Levine, Marci; Scholdberg, Tandace; Haynes, Ross J; Jenkins, G Ronald
Development of antivirals has focused primarily on vaccines and on treatments for specific viral agents. Although effective, these approaches may be limited in situations where the etiologic agent is unknown or when the target virus has undergone mutation, recombination or reassortment. Augmentation of the innate immune response may be an effective alternative for disease amelioration. Nonspecific, broad-spectrum immune responses can be induced by double-stranded (ds)RNAs such as poly (ICLC), or oligonucleotides (ODNs) containing unmethylated deocycytidyl-deoxyguanosinyl (CpG) motifs. These may offer protection against various bacterial and viral pathogens regardless of their genetic makeup, zoonotic origin or drug resistance.
Christopher, Mary E.; Wong, Jonathan P.
Worldwide viral hepatitis is the most common cause of jaundice, chronic liver disease cirrhosis and hepatocellular carcinoma. While important advances have been made in prevention of viral hepatitis, therapy of this disease remains unsatisfactory. There are no specific therapies of proven benefit for acute hepatitis, although use of alpha-interferon during the acute phase of hepatitis C may result in a
Jay H. Hoofnagle
Viral infections induce multiple perturbations that spread along the links of the biological networks of the host cells. Understanding the impact of these cascading perturbations requires an exhaustive knowledge of the cellular machinery as well as a systems biology approach that reveals how individual components of the cellular system function together. Here we describe an integrative method that provides a new approach to studying virus-human interactions and its correlations with diseases. Our method involves the combined utilization of protein - protein interactions, protein -- DNA interactions, metabolomics and gene - disease associations to build a ``viraldiseasome''. By solely using high-throughput data, we map well-known viral associated diseases and predict new candidate viral diseases. We use microarray data of virus-infected tissues and patient medical history data to further test the implications of the viral diseasome. We apply this method to Epstein-Barr virus and Human Papillomavirus and shed light into molecular development of viral diseases and disease pathways.
Gulbahce, Natali; Yan, Han; Vidal, Marc; Barabasi, Albert-Laszlo
Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.
Integrating viral gene delivery with engineered biomaterials is a promising strategy to overcome a number of challenges associated with virus-mediated gene delivery, including inefficient delivery to specific cell types, limited tropism, spread of vectors to distant sites, and immune responses. Viral vectors can be combined with biomaterials either through encapsulation within the material or immobilization onto a material surface. Subsequent
Jae-Hyung Jang; David V Schaffer; Lonnie D Shea
Designs of multilayer antireflection coatings made from co-sputtered and low-refractive-index materials are optimized using a genetic algorithm. Co-sputtered and low-refractive-index materials allow the fine-tuning of refractive index, which is required to achieve optimum anti-reflection characteristics. The algorithm minimizes reflection over a wide range of wavelengths and incident angles, and includes material dispersion. Designs of antireflection coatings for silicon-based image sensors and solar cells, as well as triple-junction GaInP/GaAs/Ge solar cells are presented, and are shown to have significant performance advantages over conventional coatings. Nano-porous low-refractive-index layers are found to comprise generally half of the layers in an optimized antireflection coating, which underscores the importance of nano-porous layers for high-performance broadband and omnidirectional antireflection coatings. PMID:18542630
Schubert, Martin F; Mont, Frank W; Chhajed, Sameer; Poxson, David J; Kim, Jong Kyu; Schubert, E Fred
Adenoviruses are globally spread and infect species in all five taxons of vertebrates. Outstanding attention is focused on adenoviruses because of their transformation potential, their possible usability as vectors in gene therapy and their applicability in studies dealing with, e.g. cell cycle control, DNA replication, transcription, splicing, virus–host interactions, apoptosis, and viral evolution. The accumulation of genetic data provides the
Udo Bahr; Eva Schöndorf; Michaela Handermann; Gholamreza Darai
We present a new definition of the concept of representation for cognitive science that is based on a study of the origin of structures that are used to store memory in evolving systems. This study consists of novel computer experiments in the evolution of cellular automata to perform nontrivial tasks as well as evidence from biology concerning genetic memory. Our
Luis Mateus Rocha; Wim Hordijk
Genetic algorithms (GAs) are a tool used to solve high-complexity computational problems. Apart from modelling the phenomena occurring in Nature, they help in optimization, simulation, modelling, design and prediction purposes in science, medicine, technology, and everyday life. They can be adapted to the given task, be joined with other ones (this leads to combined or hybrid methods), and can work
The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.
Phan, Tung G.; Kapusinszky, Beatrix; Wang, Chunlin; Rose, Robert K.; Lipton, Howard L.; Delwart, Eric L.
Advancements in diagnostic methods, particularly polymerase chain reaction (PCR)-based testing of cerebrospinal fluid for viral nucleic acids, have diminished the role of neuropathologic examination in the diagnosis of viral infections of the central nervous system (CNS). Nevertheless, neuropathologic examination of CNS tissue remains important in the diagnosis of atypical viral encephalitides and in the exclusion of non-infectious etiologies. In addition to routine hematoxylin and eosin stains on tissue sections, the neuropathologist may utilize immunohistochemistry, in situ hybridization, electron microscopy, and PCR-based testing of the tissue specimen. In this review, we cover the general pathologic features of viral infections of the CNS as well as the specific features of CNS infections caused by poliovirus, herpes simplex virus, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, rabies virus, West Nile virus, Eastern equine encephalitis virus, measles virus, JC virus, human immunodeficiency virus, and human T lymphotropic virus type 1. PMID:25015486
Hatanpaa, Kimmo J; Kim, Jung H
Gene therapy has great potential to treat or prevent a variety of both genetic and acquired conditions that include neuromuscular disorders, cardiovascular disease, cancer, and infectious diseases. For recessive genetic disorders such as Duchenne muscular dystrophy, delivery of the normal dystrophin gene to muscle should prevent the myofibers from dying. Despite the great promise and sound principles of gene therapy, its application to humans have been hampered by the inability to safely and effectively deliver genes to the target tissues. Among the several gene transfer methods under development, the use of non-viral delivery methods and specifically naked DNA is particularly attractive in that many of the concerns over the use of viral-mediated methods, such as immunogenicity of viral packaging proteins and cost of viral vector production can be avoided. Recently we used limb veins for efficient, repeatable, and safe delivery of nucleic acids to skeletal myofibers throughout the limb muscles of mammals in vivo. Promising results have been obtained in both rodents and larger animals including non-human primates. Studies in the mdx mouse model indicate that the approach should be of use for patients with Duchenne muscular dystrophy. Based upon these encouraging results, a human clinical trial to deliver the human dystrophin gene to patients with DMD is being planned. The initial objective is to preserve hand and forearm function to increase the quality of life. PMID:16629054
Wolff, J; Lewis, D L; Herweijer, H; Hegge, J; Hagstrom, J
The cyanobacterial radiation consists of several lineages of phyletically (morphologically and genetically) related organisms. Several of these organisms show a striking resemblance to fossil counterparts. To inves- tigate the molecular mechanisms responsible for stabilizing or homogenizing cyanobacterial characters, we compared the evolutionary rates and phylogenetic origins of the small-subunit rRNA-encoding DNA (16S rDNA), the conserved gene rbcL (encoding D-ribulose 1,5-bisphosphate
KNUT RUDI; OLAV M. SKULBERG; KJETILL S. JAKOBSEN
Infection by viruses having lipid-bilayer envelopes proceeds through fusion of the viral membrane with a membrane of the target cell. Viral 'fusion proteins' facilitate this process. They vary greatly in structure, but all seem to have a common mechanism of action, in which a ligand-triggered, large-scale conformational change in the fusion protein is coupled to apposition and merger of the
Stephen C Harrison
Viral Marketing beschreibt das gezielte Auslösen von Mundpropaganda zum Zwecke der Vermarktung von Unternehmen und deren Leistungen.\\u000a Viral Marketing baut auf den Forschungsergebnissen unterschiedlicher Wissenschaftszweige wie etwa der Psychologie, der Sozialwissenschaften\\u000a oder der Evolutionstheorie auf und integriert Erfahrungen der unternehmerischen Praxis. Dadurch entstand in den letzten Jahren\\u000a ein Arsenal an Strategien und Taktiken zur Planung, Durchführung und Erfolgsmessung von Marketingaktionen,
Viral infections of the central nervous system are uncommon but are important in the differential diagnosis of acute myelopathy.\\u000a Acute viral myelitis can present as acute flaccid paralysis (poliomyelitis) or neurologic dysfunction due to involvement of\\u000a the white matter. The latter usually affects only part of the transverse expanse of the spinal cord and manifests as asymmetric\\u000a motor and sensory
Octavia Kincaid; Howard L. Lipton
Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences.
Human immunodeficiency virus type 1 (HIV-1) sequences were generated from blood and from brain tissue obtained by stereotactic biopsy from six patients undergoing a diagnostic neurosurgical procedure. Proviral DNA was directly amplified by nested PCR, and 8 to 36 clones from each sample were sequenced. Phylogenetic analysis of intrapatient envelope V3-V5 region HIV-1 DNA sequence sets revealed that brain viral sequences were clustered relative to the blood viral sequences, suggestive of tissue-specific compartmentalization of the virus in four of the six cases. In the other two cases, the blood and brain virus sequences were intermingled in the phylogenetic analyses, suggesting trafficking of virus between the two tissues. Slide-based PCR-driven in situ hybridization of two of the patients' brain biopsy samples confirmed our interpretation of the intrapatient phylogenetic analyses. Interpatient V3 region brain-derived sequence distances were significantly less than blood-derived sequence distances. Relative to the tip of the loop, the set of brain-derived viral sequences had a tendency towards negative or neutral charge compared with the set of blood-derived viral sequences. Entropy calculations were used as a measure of the variability at each position in alignments of blood and brain viral sequences. A relatively conserved set of positions were found, with a significantly lower entropy in the brain-than in the blood-derived viral sequences. These sites constitute a brain "signature pattern," or a noncontiguous set of amino acids in the V3 region conserved in viral sequences derived from brain tissue. This brain-derived signature pattern was also well preserved among isolates previously characterized in vitro as macrophage tropic. Macrophage-monocyte tropism may be the biological constraint that results in the conservation of the viral brain signature pattern. Images
Korber, B T; Kunstman, K J; Patterson, B K; Furtado, M; McEvilly, M M; Levy, R; Wolinsky, S M
A bifunctional protein composed of a highly negatively charged oyster shell protein and a chitin-binding domain enabled the formation of biohybrid materials through non-covalent surface modification of chitin nanofibres. The results demonstrate that specific biomolecular interactions offer a route for the formation of biosynthetic materials. PMID:24871427
Malho, Jani-Markus; Heinonen, Hanna; Kontro, Inkeri; Mushi, Ngesa E; Serimaa, Ritva; Hentze, Hans-Peter; Linder, Markus B; Szilvay, Géza R
Important role of prodromal viral infections responsible for inhibition of xenobiotic metabolizing enzymes in the pathomechanism of idiopathic Reye's syndrome, Stevens-Johnson syndrome, autoimmune hepatitis, and hepatotoxicity of the therapeutic doses of acetaminophen used in genetically predisposed persons.
Upper respiratory tract febrile illnesses caused by various viruses, mycoplasma, chlamydia infections, and/or inflammatory diseases are usually observed a few days to a few (several) weeks before the onset of Reye's syndrome, Stevens-Johnson syndrome, autoimmune hepatitis (hepatotropic virus infections), or hepatotoxicity associated with therapeutic administration of acetaminophen in persons with varying degrees of deficits of important enzymatic activity. Activation of systemic host defense mechanisms by inflammatory component(s) results in depression of various induced and constitutive isoforms of cytochrome P-450 mixed-function oxidase system superfamily enzymes in the liver and most other tissues of the body. Because several cytochrome P-450 enzymes activities important for biotransformation of many endogenous and egzogenous substances show considerable variability between individuals, in some genetically predisposed persons, even the administration of therapeutic doses of a drug may result in serious clinical mishaps, if an important concomitant risk factor (eg, acute viral infection) is involved. Several inflammatory cytokines, such as interleukins, transforming growth factor beta1, human hepatocyte growth factor, and lymphotoxin, downregulate gene expression of major cytochrome P-450 enzymes with the specific effects on mRNA levels, protein expression, and enzyme activity observed with a given cytokine varying for each P-450 studied, thus eventually leading to metabolite-mediated adverse drug reactions and immunometallic diseases which sometimes result in tissue injury beyond the site(s) where metabolic bioactivation takes place. On the other hand, it must be emphasized that inhibition of metabolism of several drugs, as well as influence on the concentration and/or ratio of various cytokines in inflamed tissues, may exert beneficial effects in patients with different diseases, thus opening new therapeutic possibilities. Clinically relevant interactions may be exemplified by the effects of some fluoroquinolone antibiotics, such as pefloxacin and ciprofloxacin, which probably have a steroid-sparing effect in some patients with frequently relapsing nephrotic syndrome, and an increased bioavailability of several drugs following concomitant intake with freshly pressed grapefruit juice, eventually caused by inhibition of their metabolism, mediated mainly by CYP3A and specifically inhibited by naturally occurring flavonoids. PMID:11897929
The economic importance of bovine viral diarrhea is increasing with the emergence of seemingly more virulent viruses, as evidenced by outbreaks of hemorrhagic syndrome and severe acute bovine viral diarrhea beginning in the 1980s and 1990s. It appears that evolutionary changes in bovine viral diarrhea virus were responsible for these outbreaks. The genetic properties of the classical bovine viral diarrhea virus that contribute to the basis of current diagnostic tests, vaccines, and our understanding of pathogenic mechanisms are now being reevaluated because of these “new” virus strains. This shift in virulence has confounded both nomenclature and the significance of current bovine viral diarrhea virus categorization. The purpose of this review is to summarize our current understanding of bovine viral diarrhea virus with a chronological review of prevailing scientific tenets and practices as described in clinical and scientific North American veterinary journals and textbooks. The first part of this review describes how we have arrived at our current understanding of the viruses, the diseases, and their nomenclature. The second part of the review deals with current concepts in virology and how these concepts may both explain and predict bovine viral diarrhea virus pathogenesis. By reviewing how knowledge of bovine viral diarrhea has evolved and the theories of how the virus itself is able to evolve, the interpretation of diagnostic tests are more effectively utilized in the control and treatment of bovine viral diarrhea virus associated disease.
Motivation: Next-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors. Results: In this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Highly accurate data in combination with deep coverage allow VGA to assemble rare variants. VGA uses an expectation–maximization algorithm to estimate abundances of the assembled viral variants in the population. Results on both synthetic and real datasets show that our method is able to accurately assemble an HIV viral population and detect rare variants previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for genome-wide viral assembly. Furthermore, our method is the first viral assembly method that scales to millions of sequencing reads. Availability: Our tool VGA is freely available at http://genetics.cs.ucla.edu/vga/ Contact: email@example.com; firstname.lastname@example.org
Mangul, Serghei; Eskin, Eleazar
Deoxyribonucleate (DNA) preparations were extracted from Neisseria meningitidis (four isolates from spinal fluid and blood) and N. gonorrhoeae strains, all of which were resistant to sulfadiazine upon primary isolation. These DNA preparations, together with others from in vitro mutants of N. meningitidis and N. perflava, were examined in transformation tests by using as recipient a drug-susceptible strain of N. meningitidis (Ne 15 Sul-s Met+) which was able to grow in a methionine-free defined medium. The sulfadiazine resistance typical of each donor was introduced into the uniform constitution of this recipient. Production of p-aminobenzoic acid was not significantly altered thereby. Transformants elicited by DNA from the N. meningitidis clinical isolates were resistant to at least 200 ?g of sulfadiazine/ml, and did not show a requirement for methionine (Sul-r Met+). DNA from six strains of N. gonorrhoeae, which were isolated during the period of therapeutic use of sulfonamides, conveyed lower degrees of resistance and, invariably, a concurrent methionine requirement (Sul-r/Met?). The requirement of these transformants, and that of in vitro mutants selected on sulfadiazine-agar, was satisfied by methionine, but not by vitamin B12, homocysteine, cystathionine, homoserine, or cysteine. Sul-r Met+ and Sul-r/Met? loci could coexist in the same genome, but were segregated during transformation. On the other hand, the dual Sul-r/Met? properties were not separated by recombination, but were eliminated together. DNA from various Sul-r/Met? clones tested against recipients having nonidentical Sul-r/Met? mutant sites yielded Sul-s Met+ transformants. The met locus involved is genetically complex, and will be a valuable tool for studies of genetic fine structure of members of Neisseria, and of genetic homology between species. Images
Catlin, B. Wesley
... attched to a sugar phosphate backbone. What is DNA? DNA, or deoxyribonucleic acid, is the hereditary material in ... cell in a person's body has the same DNA. Most DNA is located in the cell nucleus ( ...
Background Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods In the present study we evaluated the viral diversity of fecal samples (n?=?42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.
This document traces the history of the samples used in the genetic and animal toxicity testing of SRC products, process intermediates, and waste materials. It begins with a brief summary (Table G-1, page G.1.2), which indicates the source, further processing, storage, and transmittals of all sample materials used in the testing. This summary is followed by more detailed descriptions of
B. Z. Drozdowicz; C. M. Kelly
Viral oncolytic therapy has been pursued with renewed interest as the molecular basis of carcinogenesis and viral replication has been elucidated. Genetically engineered, attenuated viruses have been rationally constructed to achieve a therapeutic index in tumor cells compared with surrounding normal tissue. Many of these attenuated mutant viruses have entered clinical trials. Here we review the preclinical literature demonstrating the interaction of oncolytic viruses with ionizing radiation and provides a basis for future clinical trials.
Advani, Sunil J. [Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL (United States); Mezhir, James J. [Department of Surgery, University of Chicago, Chicago, IL (United States); Roizman, Bernard [Marjorie B. Kovler Viral Oncology Laboratories, University of Chicago, Chicago, IL (United States); Weichselbaum, Ralph R. [Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL (United States)]. E-mail: email@example.com
We develop biophysical models of viral infections from a stochastic process perspective. The entry of enveloped viruses is treated as a stochastic multiple receptor and coreceptor engagement process that can lead to membrane fusion or endocytosis. The probabilities of entry via fusion and endocytosis are computed as functions of the receptor/coreceptor engagement rates. Since membrane fusion and endocytosis entry pathways can lead to very different infection outcomes, we delineate the parameter regimes conducive to each entry pathway. After entry, viral material is biochemically processed and degraded as it is transported towards the nucleus. Productive infections occur only when the material reaches the nucleus in the proper biochemical state. Thus, entry into the nucleus in an infectious state requires the proper timing of the cytoplasmic transport process. We compute the productive infection probability and show its nonmonotonic dependence on both transport speeds and biochemical transformation rates. Our results carry subtle consequences on the dosage and efficacy of antivirals such as reverse transcription inhibitors.
Viral hepatitis is a serious health problem all over the world. The aim of the study is to present the actual achievements in the therapeutically field and the general knowledge concerning the subject. Are presented the etiological agents of the acute and chronic hepatitis with the focus on hepatitis B and C, which has become a priority of WHO, with an incidence of the diseases of 360 billion/year for hepatitis B and an sub estimated level for C hepatitis. The most used drugs are presented and the therapeutical combination meant to decrease biological and virusological markers (ALAT, viral load) and to ameliorate the histological aspects of the liver. In conclusion, acute and chronic viral hepatitis represents a challenge for epidemiologists who try to stop the spread of the disease, but also for the infectious diseases specialists and gastroenterologists. PMID:20700962
Manciuc, Carmen; Dorob??, Carmen; Filip-Ciubotaru, Florina-Mihaela
Models describing acoustic properties of porous materials involve quantities, such us characteristic impedance Zc and complex wave number kc, that in turn involve physical parameters (i. e. flow resistivity, tortuosity and porosity). These parameters should be either measured or estimated from measures of acoustic quantities such as the normal incidence absorption coefficient. Unfortunately, direct measurements of theses parameters are often
M. Garoum; M. Rhachi; F. Simón; A. Moreno
Genetic and chemical engineering approaches are used to employ P22 viral capsids as nanoplatforms for developing an efficient delivery vehicle. Catechol ligands are chemically attached to the interior surface of P22 viral capsid for subsequent encapsulation of an anticancer drug, bortezomib (BTZ), through boronic acid-diol complexation. For targeted delivery, hepatocellular carcinoma (HCC)-targeting peptide (SP94, SFSIIHTPILPL) is synthesized and chemically conjugated to the exterior surface of the P22 viral capsid nanocomposites. Effective targeted delivery of synthesized P22 viral capsid nanocomposites is demonstrated by fluorescent cell imaging and the efficacy of delivered P22 viral capsid nanocomposites is evaluated using a cell viability assay. PMID:24847525
Min, Junseon; Moon, Hyojin; Yang, Hyun Ji; Shin, Hyun-Hee; Hong, Sung You; Kang, Sebyung
Viral nanotechnology is an emerging and highly interdisciplinary field in which viral nanoparticles (VNPs) are applied in diverse areas such as electronics, energy and next-generation medical devices. VNPs have been developed as candidates for novel materials, and are often described as “programmable” because they can be modified and functionalized using a number of techniques. In this review, we discuss the concepts and methods that allow VNPs to be engineered, including (i) bioconjugation chemistries, (ii) encapsulation techniques, (iii) mineralization strategies, and (iv) film and hydrogel development. With all these techniques in hand, the potential applications of VNPs are limited only by the imagination.
Pokorski, Jonathan K.; Steinmetz, Nicole F.
The target-independent identification of viral pathogens using 'shotgun' metagenomic sequencing is an emerging approach with potentially wide applications in clinical diagnostics, public health monitoring, and viral discovery. In this approach, all viral nucleic acids present in a sample are sequenced in a random, shotgun manner. Pathogens are then identified without the prerequisite of searching for a specific viral pathogen. In this opinion article, I discuss the current state and future research directions for this emerging and disruptive technology. With further technical developments, viral metagenomics has the potential to be deployed as a powerful and widely adopted tool, transforming the way that viral disease is researched, monitored, and treated. PMID:23415279
Qualitative polymerase chain reaction methods for the detection of genetically modified potatoes have been investigated that can be used for screening purposes and identification of insect-resistant and virus-resistant potatoes in food. The presence of the nos terminator from Agrobacterium tumefaciens and the antibiotic marker gene nptII (neomycin-phosphotransferase II) was demonstrated in three commercialized Bt-potato lines (Monsanto Co., St. Louis, MO, USA) and one noncommercial GM-potato product (high amylopectin starch, AVEBE, Veendam, The Netherlands) and allows for general screening in foods. For further identification, specific primers for the FMV promoter derived from the figwort mosaic virus, the CryIIIA gene (delta-endotoxin from Bacillus thuringiensis subsp. tenebrionis), potato leafroll virus replicase gene, and the potato virus Y coat protein gene, were designed. The methods described were successfully applied to processed potato raw materials (dehydrated potato powders and flakes), starch samples, and finished products. PMID:12537422
Jaccaud, Etienne; Höhne, Michaela; Meyer, Rolf
PNA is a pseudopeptide DNA mimic in which the natural nucleobases have been retained, but the backbone consists of N-(2-aminoethyl)glycine units to which the nucleobases are attached via methylene carbonyl linkers. The finding that PNA forms Warson-Crick-like helices with complementary DNA, RNA or PNA combined with the fact PNA is held together by amide bonds has made PNA of interest as a model for a primordial genetic material. Furthermore, the PNA backbone is achiral, while preferred chirality can be induced in PNA-PNA double helices by attached chiral ligands, thereby providing a new way of ``chiral amplification.'' Finally, it has been demonstrated that PNA-template directed synthesis of RNA and PNA is feasible.
Nielsen, Peter E.
Viruses hijack host factors for their high speed protein synthesis, but information about these factors is largely unknown. In searching for genes that are involved in viral replication, we carried out a forward genetic screen for Drosophila mutants that are more resistant or sensitive to Drosophila C virus (DCV) infection-caused death, and found a virus-resistant line in which the expression of pelo gene was deficient. Our mechanistic studies excluded the viral resistance of pelo deficient flies resulting from the known Drosophila anti-viral pathways, and revealed that pelo deficiency limits the high level synthesis of the DCV capsid proteins but has no or very little effect on the expression of some other viral proteins, bulk cellular proteins, and transfected exogenous genes. The restriction of replication of other types of viruses in pelo deficient flies was also observed, suggesting pelo is required for high level production of capsids of all kinds of viruses. We show that both pelo deficiency and high level DCV protein synthesis increase aberrant 80S ribosomes, and propose that the preferential requirement of pelo for high level synthesis of viral capsids is at least partly due to the role of pelo in dissociation of stalled 80S ribosomes and clearance of aberrant viral RNA and proteins. Our data demonstrated that pelo is a host factor that is required for high efficiency translation of viral capsids and targeting pelo could be a strategy for general inhibition of viral infection.
Wu, Xiurong; He, Wan-Ting; Tian, Shuye; Meng, Dan; Li, Yuanyue; Chen, Wanze; Li, Lisheng; Tian, Lili; Zhong, Chuan-Qi; Han, Felicia; Chen, Jianming; Han, Jiahuai
The diagnosis of viral infections by culture relies on the collection of proper specimens, proper care to protect the virus in the specimens from environmental damage, and use of an adequate transport system to maintain virus activity. Collection of specimens with swabs that are toxic to either virus or cell culture should be avoided. A variety of transport media have been formulated, beginning with early bacteriological transport media. Certain swab-tube combinations have proven to be both effective and convenient. Of the liquid transport media, sucrose-based and broth-based media appear to be the most widely accepted and used. Studies on virus stability show that most viruses tested are sufficiently stable in transport media to withstand a transport time of 1 to 3 days. Some viruses may withstand longer transport times. In many cases, it is not necessary to store virus specimens in a refrigerator or send them to the laboratory on wet ice or frozen on dry ice. However, the specimen should not be exposed to environmental extremes. Modern viral transport media allow for more effective use of viral culture and culture enhancement techniques for the diagnosis of human viral infections.
Johnson, F B
In an analogous system to mammals, induction of an apoptotic cell death programme (PCD) in yeast is not only restricted to various exogenous factors and stimuli, but can also be triggered by viral killer toxins and viral pathogens. In yeast, toxin secreting killer strains are frequently infected with double-stranded (ds)RNA viruses that are responsible for killer phenotype expression and toxin secretion in the infected host. In most cases, the viral toxins are either pore-forming proteins (such as K1, K2, and zygocin) that kill non-infected and sensitive yeast cells by disrupting cytoplasmic membrane function, or protein toxins (such as K28) that act in the nucleus by blocking DNA synthesis and subsequently causing a G1/S cell cycle arrest. Interestingly, while all these virus toxins cause necrotic cell death at high concentration, they trigger caspase- and ROS-mediated apoptosis at low-to-moderate concentration, indicating that even low toxin doses are deadly by triggering PCD in enemy cells. Remarkably, viral toxins are not solely responsible for cell death induction in vivo, as killer viruses themselves were shown to trigger apoptosis in non-infected yeast. Thus, as killer virus-infected and toxin secreting yeasts are effectively protected and immune to their own toxin, killer yeasts bear the intrinsic potential to dominate over time in their natural habitat. PMID:18291112
Schmitt, Manfred J; Reiter, Jochen
One method of viral marketing involves seeding certain consumers within a population to encourage faster adoption of the product throughout the entire population. However, determining how many and which consumers within a particular social network should be seeded to maximize adoption is challenging. We define a strategy space for consumer seeding by weighting a combination of network characteristics such as
Forrest Stonedahl; William Rand; Uri Wilensky
Defensins are antimicrobial peptides important to innate host defense. In addition to their direct antimicrobial effect, defensins modulate immune responses. Increasing evidence indicates that defensins exhibit complex functions by positively or negatively modulating infections of both enveloped and non-enveloped viruses. The effects of defensins on viral infections appear to be specific to the defensin, virus and target cell. Regulation of
Jian Ding; Yi-Ying Chou; Theresa L. Chang
Viral and protozoan pathogens associated with raw sludge can cause encephalitis, gastroenteritis, hepatitis, myocarditis, and a number of other diseases. Raw sludge that has been treated to reduce these pathogens can be used for land application according to the regulations spec...
The increasing use of viral stealth marketing as a contemporary marketing technique is not well represented in empirical research, particularly in examining consumers' attitudes towards the ethics and effectiveness of viral stealth marketing. Capitalizing on the efficacy of the electronic medium, viral stealth marketing seeks to disguise the relationship between the individual(s) conveying the message and the organisation endorsing it.
Celeste Swanepoel; Ashley Lye; Robert Rugimbana
Primary (spontaneous and externally induces) damages to genetic material frequently lead to heritable changes (gene mutations, chromosome aberrations and nondisjunction), which may cause cancer inherent and inborn diseases. It is suggested that primary damages may affect a phenotype until they are repaired or become mutations during inaccurate repair The alpha-test on the yeast Saccharomyces cerevisiae can answer the fundamental questions as the nature of primary damages that can be phenotypically manifested, their occurrence, conversion to each other and repair or conversion to heritable changes in genetic material. PMID:22250397
Stepchenkova, E I; Kochenova, O V; Zhuk, A S; Andre?chuk, Iu V; Inge-Vechtomov, S G
... condition may be triggered by something in the environment. In particular, viral or bacterial infections, which activate the immune system, may have the potential to encourage the development of Sjögren syndrome in susceptible individuals. The genetic ...
Acute respiratory infection is the most common disease occurring over a person's lifetime, with etiological variations determined mainly by age, environmental circumstances, the healthcare setting, and the underlying pathology. More than 200 different viruses distributed in six viral families have been implicated in the pathogenesis of respiratory tract infection. These facts are generating an increasing diagnostic demand that should be incorporated into the healthcare setting without delay. To meet this demand, the Spanish Society of Infectious Diseases and Clinical Microbiology has updated its Standard Procedure for the microbiological diagnosis of viral respiratory infection. This document contains an update primarily of infections caused by influenza viruses, and secondarily, infections due to other conventional and emerging respiratory viruses. In all cases, the methods for direct virological diagnosis (cell culture, and detection of antigens and nucleic acid) are reviewed, with special reference to techniques for molecular detection and genetic characterization. PMID:19306718
Eiros, José M; Ortiz de Lejarazu, Raúl; Tenorio, Alberto; Casas, Inmaculada; Pozo, Francisco; Ruiz, Guillermo; Pérez-Breña, Pilar
Upon viral infection, the major defensive strategy employed by the host immune system is the activation of the interferon (IFN)-mediated antiviral pathway, which is overseen by IFN regulatory factors (IRFs). In order to complete their life cycles, viruses must find a way to modulate the host IFN-mediated immune response. Kaposi's sarcoma-associated herpesvirus (KSHV), a human tumor-inducing herpesvirus, has developed a unique mechanism for antagonizing cellular IFN-mediated antiviral activity by incorporating viral homolog of the cellular IRFs, called vIRFs, into its genome. Here, we summarize the novel evasion mechanisms by which KSHV, through its vIRFs, circumvents IFN-mediated innate immune responses and deregulates the cell growth control mechanism.
Kim, Myung Hee; Lee, Jong-Soo; Liang, Chengyu; Jung, Jae U.
Upon viral infection, the major defensive strategy employed by the host immune system is the activation of the interferon (IFN)-mediated antiviral pathway, which is overseen by IFN regulatory factors (IRFs). In order to complete their life cycles, viruses must find a way to modulate the host IFN-mediated immune response. Kaposi's sarcoma-associated herpesvirus (KSHV), a human tumor-inducing herpesvirus, has developed a unique mechanism for antagonizing cellular IFN-mediated antiviral activity by incorporating viral homolog of the cellular IRFs, called vIRFs, into its genome. Here, we summarize the novel evasion mechanisms by which KSHV, through its vIRFs, circumvents IFN-mediated innate immune responses and deregulates the cell growth control mechanism. PMID:19715458
Lee, Hye-Ra; Kim, Myung Hee; Lee, Jong-Soo; Liang, Chengyu; Jung, Jae U
Opinion statement Despite the availability of vaccines against hepatitis A and B, acute viral hepatitis due to these agents continues to be\\u000a among the most commonly reported notifiable infectious diseases in the United States. Currently available hepatitis A and\\u000a B vaccines are highly immunogenic and well tolerated, but vaccine coverage needs to be expanded. Use of the hepatitis A vaccine\\u000a in
Raymond S. Koff
Retroviral Recombination In Vivo: Viral Replication Patterns and Genetic Structure of Simian Immunodeficiency Virus (SIV) Populations in Rhesus Macaques after Simultaneous or Sequential Intravaginal Inoculation with SIVmac239 vpx\\/ vpr and SIVmac239 nef
To characterize the occurrence, frequency, and kinetics of retroviral recombination in vivo, we intravaginally inoculated rhesus macaques, either simultaneously or sequentially, with attenuated simian immunodeficiency virus (SIV) strains having complementary deletions in their accessory genes and various degrees of replication impairment. In monkeys inoculated simultaneously with SIVmac239vpx\\/vpr and SIVmac239nef, recombi- nant wild-type (wt) virus and wild-type levels of plasma viral
Eun-Young Kim; Marc Busch; Kristina Abel; Linda Fritts; Patty Bustamante; Jenny Stanton; Ding Lu; Samuel Wu; Jenny Glowczwskie; Tracy Rourke; Derek Bogdan; Mike Piatak; J. D. Lifson; R. C. Desrosiers; S. Wolinsky; C. J. Miller
The dynamics of HIV-1 viremia is a complex and evolving landscape with clinical and epidemiological (public health) implications. Most studies have relied on the use of set-point viral load (VL) as a readily available proxy of viral dynamics to assess host and viral correlates. This review highlights recent findings from population-based studies of set-point VL, focusing primarily on robust data related to host genetics. A comprehensive understanding of viral dynamics will clearly need to consider both host and viral characteristics, with close attention to (i) the timing of VL measurements, (ii) the biology of viral evolution, (iii) compartments of active viral replication, (iv) the transmission source partner as the immediate past microenvironment, and (v) proper application of statistical models.
Prentice, Heather A.; Tang, Jianming
Primary central nervous system (CNS) tumors cause significant morbidity and mortality in both adults and children. While some of the genetic and molecular mechanisms of neuro-oncogenesis are known, much less is known about possible epigenetic contributions to disease pathophysiology. Over the last several decades, chronic viral infections have been associated with a number of human malignancies. In primary CNS malignancies, two families of viruses, namely polyomavirus and herpesvirus, have been detected with varied frequencies in a number of pediatric and adult histological tumor subtypes. However, establishing a link between chronic viral infection and primary CNS malignancy has been an area of considerable controversy, due in part to variations in detection frequencies and methodologies used among researchers. Since a latent viral neurotropism can be seen with a variety of viruses and a widespread seropositivity exists among the population, it has been difficult to establish an association between viral infection and CNS malignancy based on epidemiology alone. While direct evidence of a role of viruses in neuro-oncogenesis in humans is lacking, a more plausible hypothesis of neuro-oncomodulation has been proposed. The overall goals of this review are to summarize the many human investigations that have studied viral infection in primary CNS tumors, discuss potential neuro-oncomodulatory mechanisms of viral-associated CNS disease and propose future research directions to establish a more firm association between chronic viral infections and primary CNS malignancies. PMID:20387126
Saddawi-Konefka, Robert; Crawford, John R
When the error rate during the copying of genetic material exceeds a threshold value, the genetic information cannot be maintained. This concept is the basis of a new antiviral strategy termed lethal mutagenesis or virus entry into error catastrophe. Critical for its success is preventing survival of residual infectious virus or virus mutants that escape the transition into error catastrophe.
Claudia Gonzalez-Lopez; Armando Arias; Nonia Pariente; Gema Gomez-Mariano; Esteban Domingo
The aim of this study was to conduct a systematic review on the photoinactivators used in hemotherapy, with action on viral genomes. The SciELO, Science Direct, PubMed and Lilacs databases were searched for articles. The inclusion criterion was that these should be articles on inactivators with action on genetic material that had been published between 2000 and 2010. The key words used in identifying such articles were "hemovigilance", "viral inactivation", "photodynamics", "chemoprevention" and "transfusion safety". Twenty-four articles on viral photoinactivation were found with the main photoinactivators covered being: methylene blue, amotosalen HCl, S-303 frangible anchor linker effector (FRALE), riboflavin and inactin. The results showed that methylene blue has currently been studied least, because it diminishes coagulation factors and fibrinogen. Riboflavin has been studied most because it is a photoinactivator of endogenous origin and has few collateral effects. Amotosalen HCl is effective for platelets and is also used on plasma, but may cause changes both to plasma and to platelets, although these are not significant for hemostasis. S-303 FRALE may lead to neoantigens in erythrocytes and is less indicated for red-cell treatment; in such cases, PEN 110 is recommended. Thus, none of the methods for pathogen reduction is effective for all classes of agents and for all blood components, but despite the high cost, these photoinactivators may diminish the risk of blood-transmitted diseases.
Sobral, Patricia Marial; Barros, Artur Emilio de Lima; Gomes, Ayla Maritcha Alves Silva; do Bonfim, Cristine Vieira
The equilibrium adsorption of three nucleic acids: chromosomal DNA, supercoiled plasmid DNA, and 25S rRNA, on the clay minerals, montmorillonite (M) and kaolinite (K), were studied. Adsorption of the nucleic acid on the clays was rapid and maximal after 90 min of contact time. Chromosomal DNA was adsorbed to a greater extent than plasmid DNA and RNA, and the adsorption was also greater on M than on K. Adsorption isotherms were of the L type, and a plateau was reached with all the complexes, with the exception of chromosomal DNA adsorbed on M. To determine where nucleic acids are adsorbed on clay minerals and the nature of the interaction, complexes were studied by X-ray diffraction (X-RD), electron microscopy, and Fourier transform infrared (FT-IR) spectroscopy. X-RD showed that nucleic acids did not penetrate the clay, indicating that the adsorption occurred primarily on the external surfaces of clay particles, as also suggested by electron microscopy observations. FT-IR spectra of clay-tightly bound nucleic acid complexes showed absorption bands that indicate a variation of the nucleic acids status as a consequence of their adsorption on clay. Data obtained suggested that the formation of clay-nucleic acid complex could have an important role in the preservation of genetic material in primeval habitats.
Franchi, Marco; Bramanti, Emilia; Morassi Bonzi, Laura; Luigi Orioli, Pier; Vettori, Cristina; Gallori, Enzo
Introduces an activity on arthropod genetics that involves phenotype and genotype identification of the creature and the construction process. Includes a list of required materials and directions to build a model arthropod. (YDS)
The use of nanomaterials has the potential to revolutionize materials science and medicine. Currently, a number of different nanoparticles are being investigated for applications in imaging and therapy. Viral nanoparticles (VNPs) derived from plants can be regarded as self-assembled bionanomaterials with defined sizes and shapes. Plant viruses under investigation in the Steinmetz lab include icosahedral particles formed by Cowpea mosaic virus (CPMV) and Brome mosaic virus (BMV), both of which are 30 nm in diameter. We are also developing rod-shaped and filamentous structures derived from the following plant viruses: Tobacco mosaic virus (TMV), which forms rigid rods with dimensions of 300 nm by 18 nm, and Potato virus X (PVX), which form filamentous particles 515 nm in length and 13 nm in width (the reader is referred to refs. (1) and (2) for further information on VNPs). From a materials scientist's point of view, VNPs are attractive building blocks for several reasons: the particles are monodisperse, can be produced with ease on large scale in planta, are exceptionally stable, and biocompatible. Also, VNPs are "programmable" units, which can be specifically engineered using genetic modification or chemical bioconjugation methods. The structure of VNPs is known to atomic resolution, and modifications can be carried out with spatial precision at the atomic level, a level of control that cannot be achieved using synthetic nanomaterials with current state-of-the-art technologies. In this paper, we describe the propagation of CPMV, PVX, TMV, and BMV in Vigna ungiuculata and Nicotiana benthamiana plants. Extraction and purification protocols for each VNP are given. Methods for characterization of purified and chemically-labeled VNPs are described. In this study, we focus on chemical labeling of VNPs with fluorophores (e.g. Alexa Fluor 647) and polyethylene glycol (PEG). The dyes facilitate tracking and detection of the VNPs, and PEG reduces immunogenicity of the proteinaceous nanoparticles while enhancing their pharmacokinetics. We demonstrate tumor homing of PEGylated VNPs using a mouse xenograft tumor model. A combination of fluorescence imaging of tissues ex vivo using Maestro Imaging System, fluorescence quantification in homogenized tissues, and confocal microscopy is used to study biodistribution. VNPs are cleared via the reticuloendothelial system (RES); tumor homing is achieved passively via the enhanced permeability and retention (EPR) effect. The VNP nanotechnology is a powerful plug-and-play technology to image and treat sites of disease in vivo. We are further developing VNPs to carry drug cargos and clinically-relevant imaging moieties, as well as tissue-specific ligands to target molecular receptors overexpressed in cancer and cardiovascular disease. PMID:23183850
Wen, Amy M; Lee, Karin L; Yildiz, Ibrahim; Bruckman, Michael A; Shukla, Sourabh; Steinmetz, Nicole F
The complement system functions as an immune surveillance system that rapidly responds to infection. Activation of the complement system by specific recognition pathways triggers a protease cascade, generating cleavage products that function to eliminate pathogens, regulate inflammatory responses, and shape adaptive immune responses. However, when dysregulated, these powerful functions can become destructive and the complement system has been implicated as a pathogenic effector in numerous diseases, including infectious diseases. This review highlights recent discoveries that have identified critical roles for the complement system in the pathogenesis of viral infection.
Stoermer, Kristina A.; Morrison, Thomas E.
During the last 15 years, several different groups of fastidious viruses that are responsible for a large proportion of acute viral gastroenteritis cases have been discovered by the electron microscopic examination of stool specimens. This disease is one of the most prevalent and serious clinical syndromes seen around the world, especially in children. Rotaviruses, in the family Reoviridae, and fastidious fecal adenoviruses account for much of the viral gastroenteritis in infants and young children, whereas the small caliciviruses and unclassified astroviruses, and possibly enteric coronaviruses, are responsible for significantly fewer cases overall. In addition to electron microscopy, enzyme immunoassays and other rapid antigen detection systems have been developed to detect rotaviruses and fastidious fecal adenoviruses in the stool specimens of both nonhospitalized patients and those hospitalized for dehydration and electrolyte imbalance. Experimental rotavirus vaccines have also been developed, due to the prevalence and seriousness of rotavirus infection. The small, unclassified Norwalk virus and morphologically similar viruses are responsible for large and small outbreaks of acute gastroenteritis in older children, adolescents, and adults. Hospitalization of older patients infected with these viruses is usually not required, and their laboratory diagnoses have been limited primarily to research laboratories. Images
Christensen, M L
Viral diseases of rabbits have been used historically to study oncogenesis (e.g. rabbit fibroma virus, cottontail rabbit papillomavirus) and biologically to control feral rabbit populations (e.g. myxoma virus). However, clinicians seeing pet rabbits in North America infrequently encounter viral diseases although myxomatosis may be seen occasionally. The situation is different in Europe and Australia, where myxomatosis and rabbit hemorrhagic disease are endemic. Advances in epidemiology and virology have led to detection of other lapine viruses that are now recognized as agents of emerging infectious diseases. Rabbit caliciviruses, related to rabbit hemorrhagic disease, are generally avirulent, but lethal variants are being identified in Europe and North America. Enteric viruses including lapine rotavirus, rabbit enteric coronavirus and rabbit astrovirus are being acknowledged as contributors to the multifactorial enteritis complex of juvenile rabbits. Three avirulent leporid herpesviruses are found in domestic rabbits. A fourth highly pathogenic virus designated leporid herpesvirus 4 has been described in Canada and Alaska. This review considers viruses affecting rabbits by their clinical significance. Viruses of major and minor clinical significance are described, and viruses of laboratory significance are mentioned. PMID:23642871
Kerr, Peter J; Donnelly, Thomas M
Integrating viral gene delivery with engineered biomaterials is a promising strategy to overcome a number of challenges associated with virus-mediated gene delivery, including inefficient delivery to specific cell types, limited tropism, spread of vectors to distant sites, and immune responses. Viral vectors can be combined with biomaterials either through encapsulation within the material or immobilization onto a material surface. Subsequent biomaterial-based delivery can increase the vector's residence time within the target site, thereby potentially providing localized delivery, enhancing transduction, and extending the duration of gene expression. Alternatively, physical or chemical modification of viral vectors with biomaterials can be employed to modulate the tropism of viruses or reduce inflammatory and immune responses, both of which may benefit transduction. This review describes strategies to promote viral gene delivery technologies using biomaterials, potentially providing opportunities for numerous applications of gene therapy to inherited or acquired disorders, infectious disease, and regenerative medicine.
Jang, Jae-Hyung; Schaffer, David V; Shea, Lonnie D
Materials play an important role in manufactured goods. Materials must possess both acceptable properties for their intended\\u000a applications and a suitable ability to be manufactured. These criteria hold true for micromanufacturing, in which parts have\\u000a overall dimensions of less than 1 mm. This chapter begins by reviewing materials usage in Asian and European research in micromanufacturing,\\u000a categorized by manufacturing process.
David Bourell; Kamlakar Rajurkar
Strain BST-1 is a derivative of Escherichia coli K-12 that carries a plasmid designated pURA-4 and is the expression system used by The Upjohn Company in the production of recombinant bovine somatotropin (rbSt). This plasmid also encodes an ampicillin resistance gene. The plasmidless carrier strain, BST-1C, contains a gene for tetracycline resistance which is provided by the chromosomal insertion of the transposon Tn10. Therefore, BST-1 is resistant to ampicillin and tetracycline, while BST-1C is resistant only to tetracycline. The Food and Drug Administration requested that we conduct an environmental assessment study to monitor the 'persistence of the recombinant live K-12 E. coli organism compared to the host E. coli organism'. In addition, we were requested to monitor 'the potential transfer of genetic material from (our) recombinant organism to the indigenous microflora' of the mouse gastrointestinal (GI) tract. The differences in persistence were determined by monitoring shedding of BST-1 and BST-1C in the feces of conventionally reared, outbred mice inoculated with either of the two strains. Even with antibiotic selective pressure applied (tetracycline in the water), BST-1 did not persist as well as the non-plasmid carrying parental stain, BST-1C. In the gene transfer experiments, transfer of pURA-4 was monitored by the appearance of the ampicillin resistance marker and/or by hybridization assays for the rbSt gene in indigenous, mouse-colonizing E. coli strains which had been made streptomycin resistant. At the limit of detection, no transfer of pURA-4 was detected either in vitro or in vivo. These data support an interpretation that BST-1 does not present an environmental hazard as measured by colonization/persistence in the gut of conventionally reared mammals. PMID:7763898
Yancey, R J; Kotarski, S F; Thurn, K K; Lepley, R A; Mott, J E
For decades, the design, development and use of metallic biomaterials has focused on the corrosion resistance of these materials once implanted in the human body. Recently, degradable metallic biomaterials (DMMs) have been proposed for some specific applications, including paediatric, orthopaedic and cardiovascular applications. DMMs are expected to disappear via corrosion after providing structural support for a certain period of time depending on the application site. Over the past decades, a wide-ranging and comprehensive set of in vitro, in vivo and for some cases also ex vivo tests have been proposed and exhaustively investigated for conventional corrosion-resistant metallic biomaterials. Standardization and regulatory bodies in the United States, Japan and Europe have therefore developed tests to license corrosion-resistant metals for use as "biomaterials". This is not the case for DMMs. Once implanted, this new class of biomaterials is expected to support the healing process of a diseased tissue or organ while degrading at a potentially adjustable degradation rate. The tests developed for corrosion-resistant metals cannot simply be transposed to DMMs. These tests can in some cases be adapted, but the expected unique properties of DMMs should also inspire and lead to the design and the development of new specific tests. The current challenge is how to assess the tolerance of surrounding tissues and organs to the presence of degradation products. This work precisely focuses on this topic. The tests usually used to assess the biocompatibility of conventional corrosion-resistant metals are briefly reviewed. Then, genetic regulation is proposed as an original and novel approach to assess the biocompatibility of DMMs. This method appears to predict cell behaviour in the presence of degradation products that are closely related to DNA damage. Various genes have been related to the toxicity and inflammatory responses, indicating their role as biomarkers to assess the toxicity of degradation products. Finally, some gene families that have the potential to be applied as biomarkers of degradation product toxicity are summarized. PMID:20176149
Purnama, Agung; Hermawan, Hendra; Couet, Jacques; Mantovani, Diego
Summary: Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant spectra or mutant clouds termed viral quasispecies. Here we review the origin of the quasispecies concept and some biological implications of quasispecies dynamics. Two main aspects are addressed: (i) mutant clouds as reservoirs of phenotypic variants for virus adaptability and (ii) the internal interactions that are established within mutant spectra that render a virus ensemble the unit of selection. The understanding of viruses as quasispecies has led to new antiviral designs, such as lethal mutagenesis, whose aim is to drive viruses toward low fitness values with limited chances of fitness recovery. The impact of quasispecies for three salient human pathogens, human immunodeficiency virus and the hepatitis B and C viruses, is reviewed, with emphasis on antiviral treatment strategies. Finally, extensions of quasispecies to nonviral systems are briefly mentioned to emphasize the broad applicability of quasispecies theory.
Sheldon, Julie; Perales, Celia
Dengue viral infections are one of the most important mosquito borne diseases in the world. They may be asymptomatic or may give rise to undifferentiated fever, dengue fever, dengue haemorrhagic fever (DHF), or dengue shock syndrome. Annually, 100 million cases of dengue fever and half a million cases of DHF occur worldwide. Ninety percent of DHF subjects are children less than 15 years of age. At present, dengue is endemic in 112 countries in the world. No vaccine is available for preventing this disease. Early recognition and prompt initiation of appropriate treatment are vital if disease related morbidity and mortality are to be limited. This review outlines aspects of the epidemiology of dengue infections, the dengue virus and its mosquito vector, clinical features and pathogenesis of dengue infections, and the management and control of these infections.
Malavige, G; Fernando, S; Fernando, D; Seneviratne, S
Topics discussed at the symposia included: Strategies of Genetic Analysis of Host Resistance; Genetic Control of Resistance to Viral Infections; Hybrid Resistance and Susceptibility to Tumor Transplants; Genetic Control of Resistance to Bacterial Infectio...
S. M. Reichard
Molecular research has vastly advanced our understanding of the mechanism of cancer growth and spread. Targeted approaches utilizing molecular science have yielded provocative results in the treatment of cancer. Oncolytic viruses genetically programmed to replicate within cancer cells and directly induce toxic effect via cell lysis or apoptosis are currently being explored in the clinic. Safety has been confirmed and
Eugene Lin; John Nemunaitis
This essay try to introduce Viral Marketing in the form of case, and through analyzing its success or failure, pros or cons, I'll make my effort to find the foothold and risk point in practice. We can see that, to be a kind of network marketing which spread by customers themselves, Viral Marketing has weak controllability and predictability. So when
Min Liu; TianShi Qu
Background Human adenoviruses (HAdVs) are the second-leading cause of childhood gastroenteritis worldwide. This virus is commonly found in environmental waters and is very resistant to water disinfection and environmental stressors, especially UV light inactivation. Molecular techniques, such as PCR-based methods (Polymerase Chain Reaction), are commonly used to detect and identify viral contamination in water, although PCR alone does not allow the discrimination between infectious and non-infectious viral particles. A combination of cell culture and PCR has allowed detection of infectious viruses that grow slowly or fail to produce cytopathic effects (CPE) in cell culture. This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system. Methods Water samples were collected, concentrated and HAdV quantified by real-time PCR. Viral integrity was evaluated by enzymatic assay (DNase I) and infectivity by plaque assay (PA) and integrated cell culture using transcribed mRNA (ICC-RT-qPCR). Samples containing particles of infectious HAdV were selected for sequencing and molecular characterization. Results The analyzed sites contained 83, 66 and 58% undamaged HAdV particles (defined as those in which the genetic material is protected by the viral capsid) at Peri Lagoon, spring source water and public supply system water, respectively. Of these, 66% of the particles (by PA) and 75% (by ICC-RT-qPCR) HAdV were shown to be infectious, due to being undamaged in Peri Lagoon, 33% (by PA) and 58% (by ICC-RT-qPCR) in spring source water and 8% (by PA) and 25% (by ICC-RT-qPCR) in the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1?×?102 HAdV genome copies per milliliter of infectious viral particles in the environmental water samples. The molecular characterization studies indicated that HAdV-2 was the prevalent serotype. Conclusions These results indicate a lack of proper public health measures. We suggest that HAdV can be efficiently used as a marker of environmental and drinking water contamination and ICC-RT-qPCR demonstrated greater sensitivity and speed of detection of infectious viral particles compared to PA.
Abnormal bone metabolism and dysfunction of the calcium-parathyroid hormone-vitamin D axis have been reported in patients with viral hepatitis. Some studies suggested a relationship between vitamin D and viral hepatitis. Genetic studies have provided an opportunity to identify the proteins that link vitamin D to the pathology of viral hepatitis (i.e., the major histocompatibility complex class II molecules, the vitamin D receptor, cytochrome P450, the renin-angiotensin system, apolipoprotein E, liver X receptor, toll-like receptor, and the proteins regulated by the Sp1 promoter gene). Vitamin D also exerts its effects on viral hepatitis via non-genomic factors, i.e., matrix metalloproteinase, endothelial vascular growth factor, prostaglandins, cyclooxygenase-2, and oxidative stress. In conclusion, vitamin D could have a beneficial role in viral hepatitis. Calcitriol is best used for viral hepatitis because it is the active form of the vitamin D3 metabolite.
Luong, Khanh vinh quoc; Nguyen, Lan Thi Hoang
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection (LRI) and viral death in infants. RSV disease in infants is characterized by epithelial desquamation, neutrophilic bronchiolitis and pneumonia and obstructive pulmonary mucus. Human rhinoviruses (HRVs) are by far the most common cause of symptomatic upper respiratory tract infection (URI) in people and are more recently appreciated as a significant cause of LRI. RSV and HRV are also implicated in asthma pathogenesis. Within both RSV and HRV, viral genetic differences play a role in disease severity and/or prevalence in patient populations, and viral genetic differences affect pathogenesis. Here, we review data on how viral genetic differences impact disease using RSV and HRV as examples, including effects on the host immune response. Virus genotype–phenotype relationships can be exploited in the laboratory to gain insight into mechanisms by which respiratory viruses modulate host immune responses and cause disease. PMID:24455766
Moore, Martin L; Stokes, Kate L; Hartert, Tina V
In the late 1970s, it was predicted that gene therapy would be applied to humans within a decade. However, despite some success, gene therapy has still not become a routine practise in medicine. In this review, we will examine the problems, both experimental and clinical, associated with the use of viral material for transgenic insertion. We shall also discuss the development of viral vectors involving the most important vector types derived from retroviruses, adenoviruses, herpes simplex viruses and adeno-associated viruses. This article is part of a themed section on Vector Design and Drug Delivery. For a list of all articles in this section see the end of this paper, or visit: http://www3.interscience.wiley.com/journal/121548564/issueyear?year=2009
Bouard, D; Alazard-Dany, N; Cosset, F-L
As biological agents, viruses come in an astounding range of sizes, with varied shapes and surface morphologies. The structures of viral capsids are generally assemblies of hundreds of copies of one or a few proteins which can be harnessed for use in a wide variety of applications in biotechnology, nanotechnology, and medicine. Despite their complexity, many capsid types form as homogenous populations of precise geometrical assemblies. This is important in both medicine, where well-defined therapeutics are critical for drug performance and federal approval, and nanotechnology, where precise placement affects the properties of the desired material. Here we review the production of viruses and virus-like particles with methods for selecting and manipulating the size, surface chemistry, assembly state, and interior cargo of capsid. We then discuss many of the applications used in research today and the potential commercial and therapeutic products from engineered viral capsids. PMID:24816622
Glasgow, Jeff; Tullman-Ercek, Danielle
Dengue viral infections are one of the most important mosquito-borne diseases in the world. Presently dengue is endemic in 112 countries in the world. It has been estimated that almost 100 million cases of dengue fever and half a million cases of dengue hemorrhagic fever (DHF) occur worldwide. An increasing proportion of DHF is in children less than 15 years of age, especially in South East and South Asia. The unique structure of the dengue virus and the pathophysiologic responses of the host, different serotypes, and favorable conditions for vector breeding have led to the virulence and spread of the infections. The manifestations of dengue infections are protean from being asymptomatic to undifferentiated fever, severe dengue infections, and unusual complications. Early recognition and prompt initiation of appropriate supportive treatment are often delayed resulting in unnecessarily high morbidity and mortality. Attempts are underway for the development of a vaccine for preventing the burden of this neglected disease. This review outlines the epidemiology, clinical features, pathophysiologic mechanisms, management, and control of dengue infections.
Gurugama, Padmalal; Garg, Pankaj; Perera, Jennifer; Wijewickrama, Ananda; Seneviratne, Suranjith L
Viral stealth marketing is electronic promotions presented as word-of-mouth communication. People spreading these messages conceal the fact that they are paid to promote a product. Non-disclosure raises important ethical questions, as well as the practical problem of the consequences of being found out. Two surveys were uploaded to social networking sites, targeted at Gen Y, with one depicting a viral-marketing
Hume Winzar; Celeste Swanepoel; Ashley Lye
I demonstrate the assembly of nanoscale viral building blocks of controlled lengths using a biologically motivated strategy. To achieve this I exploit the simple assembly mechanism of Tobacco mosaic virus (TMV), whose length is solely governed by the length of its genomic mRNA, using both the wildtype and genetically engineered (displaying cysteine residues) forms of the virus. The observed lengths of the viral building blocks correlate well with the expected lengths. Additionally, I demonstrate the assembly of viral building blocks of controlled length derived from the genetically engineered form of TMV displaying cysteine groups, which signifies that the mutation does not affect viral building block assembly. Next, I examine the application of WT viral building blocks as individual components for the assembly of 1 dimensional nanoarrays via biotin-streptavidin binding. Finally, I examine the application of genetically engineered 1cys viral building blocks as a biological template for the synthesis of metal nanoparticles, functionalization by small molecules and a component of a vertically patterned template. I envision that the biologically inspired assembly strategy to design and construct viral building blocks of controlled dimensions together with the applications explored could be employed to fabricate well-controlled nanoarchitectures and hybrid nanomaterials for a wide variety of applications.
Rego, Jennifer M.
SYNOPSIS Meningitis and myelitis represent common and very infrequent viral infections of the central nervous system (CNS), respectively. Indeed, the number of cases of viral meningitis that occurs annually exceeds the total number of meningitis cases caused by all other etiologies combined. Focal CNS infections, on the other hand, such as occur in the spinal cord with viral myelitis, are much less common and may be confused with non-infectious disorders that cause acute flaccid paralysis (AFP). This chapter will review some of the important clinical features, epidemiology, diagnostic approaches, and management strategies for patients with aseptic meningitis and viral myelitis. Particular focus will be placed on the diseases caused by enteroviruses (EVs), which as a group account for the vast majority of all aseptic meningitis cases as well as many focal infections of the spinal cord.
Irani, David N.
Viral hepatitis sera (VHS) have been shown to possess mitosis-inhibiting (MI) and chromosome damaging (CD) activities on lymphocytes cultured in vitro in presence of phytohemagglutinin. These activities can be perpetuated by serial passage with filtered m...
In this study, we analyzed viral metagenomes (viromes) in the sedimentary habitats of three geographically and geologically distinct (hado)pelagic environments in the northwest Pacific; the Izu-Ogasawara Trench (water depth?=?9,760 m) (OG), the Challenger Deep in the Mariana Trench (10,325 m) (MA), and the forearc basin off the Shimokita Peninsula (1,181 m) (SH). Virus abundance ranged from 106 to 1011 viruses/cm3 of sediments (down to 30 cm below the seafloor [cmbsf]). We recovered viral DNA assemblages (viromes) from the (hado)pelagic sediment samples and obtained a total of 37,458, 39,882, and 70,882 sequence reads by 454 GS FLX Titanium pyrosequencing from the virome libraries of the OG, MA, and SH (hado)pelagic sediments, respectively. Only 24?30% of the sequence reads from each virome library exhibited significant similarities to the sequences deposited in the public nr protein database (E-value <10?3 in BLAST). Among the sequences identified as potential viral genes based on the BLAST search, 95?99% of the sequence reads in each library were related to genes from single-stranded DNA (ssDNA) viral families, including Microviridae, Circoviridae, and Geminiviridae. A relatively high abundance of sequences related to the genetic markers (major capsid protein [VP1] and replication protein [Rep]) of two ssDNA viral groups were also detected in these libraries, thereby revealing a high genotypic diversity of their viruses (833 genotypes for VP1 and 2,551 genotypes for Rep). A majority of the viral genes predicted from each library were classified into three ssDNA viral protein categories: Rep, VP1, and minor capsid protein. The deep-sea sedimentary viromes were distinct from the viromes obtained from the oceanic and fresh waters and marine eukaryotes, and thus, deep-sea sediments harbor novel viromes, including previously unidentified ssDNA viruses.
Yoshida, Mitsuhiro; Takaki, Yoshihiro; Eitoku, Masamitsu; Nunoura, Takuro; Takai, Ken
RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines.
Stobart, Christopher C.; Moore, Martin L.
RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines. PMID:24967693
Stobart, Christopher C; Moore, Martin L
Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.
Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T. P.; Ieven, Margareta; Goossens, Herman; de Jong, Menno D.; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia
Viral hemorrhagic septicemia virus (VHSV) is considered to be one of the most important viral pathogens of finfish and is listed as reportable by many nations and international organizations (Office International des Epizooties 2006). Prior to 1988, VHSV was thought to be limited to Europe (Wolf 1988; Smail 1999). Subsequently, it was shown that the virus is endemic among many marine and anadromous fish species in both the Pacific and Atlantic Oceans (Meyers and Winton 1995; Skall et al. 2005). Genetic analysis reveals that isolates of VHSV can be divided into four genotypes that generally correlate with geographic location with the North American isolates generally falling into VHSV Genotype IV (Snow et al. 2004). In 2005-2006, reports from the Great Lakes region indicated that wild fish had experienced disease or, in some cases, very large die-offs from VHSV (Elsayed et al. 2006, Lumsden et al. 2007). The new strain from the Great Lakes, now identified as VHSV Genotype IVb, appears most closely related to isolates of VHSV from mortalities that occurred during 2000-2004 in rivers and near-shore areas of New Brunswick and Nova Scotia, Canada (Gagne et al. 2007). The type IVb isolate found in the Great Lakes region is the only strain outside of Europe that has been associated with significant mortality in freshwater species.
Winton, James; Kurath, Gael; Batts, William
Development, course and treatment of glomerulonephritis in comparison with other nephropathies was studied in 295 Hb-carriers with the nephrotic syndrome. Results of quantitative content of Hb-antigens in the blood serum and urine and nephrobiopsy materials were evaluated to show the etiopathogenetic role of Hb-viral infection in the development of glomerulonephritis. Four groups of Hb-carriers of the nephrotic syndrome were studied depending on hepatitis B markers in the blood serum. Treatment results are described in this category of patients. PMID:2011889
Bagdasarova, I V; Ivanov, D D; Ivanova, T P
Genetic defects in MOGS, the gene encoding mannosyl-oligosaccharide glucosidase (the first enzyme in the processing pathway of N-linked oligosaccharide), cause the rare congenital disorder of glycosylation type IIb (CDG-IIb), also known as MOGS-CDG. MOGS is expressed in the endoplasmic reticulum and is involved in the trimming of N-glycans. We evaluated two siblings with CDG-IIb who presented with multiple neurologic complications and a paradoxical immunologic phenotype characterized by severe hypogammaglobulinemia but limited clinical evidence of an infectious diathesis. A shortened immunoglobulin half-life was determined to be the mechanism underlying the hypogammaglobulinemia. Impaired viral replication and cellular entry may explain a decreased susceptibility to infections. PMID:24716661
Sadat, Mohammed A; Moir, Susan; Chun, Tae-Wook; Lusso, Paolo; Kaplan, Gerardo; Wolfe, Lynne; Memoli, Matthew J; He, Miao; Vega, Hugo; Kim, Leo J Y; Huang, Yan; Hussein, Nadia; Nievas, Elma; Mitchell, Raquel; Garofalo, Mary; Louie, Aaron; Ireland, Derek C; Grunes, Claire; Cimbro, Raffaello; Patel, Vyomesh; Holzapfel, Genevieve; Salahuddin, Daniel; Bristol, Tyler; Adams, David; Marciano, Beatriz E; Hegde, Madhuri; Li, Yuxing; Calvo, Katherine R; Stoddard, Jennifer; Justement, J Shawn; Jacques, Jerome; Long Priel, Debra A; Murray, Danielle; Sun, Peter; Kuhns, Douglas B; Boerkoel, Cornelius F; Chiorini, John A; Di Pasquale, Giovanni; Verthelyi, Daniela; Rosenzweig, Sergio D
Bacterial coinfections occur in respiratory viral infections, but the attack rates and the clinical profile are not clear. The aim of this study was to determine bacterial coinfections in children hospitalized for acute expiratory wheezing with defined viral etiology. A total of 220 children aged 3 months to 16 years were investigated. The viral etiology of wheezing was confirmed by viral culture,
P. Lehtinen; T. Jartti; R. Virkki; T. Vuorinen; M. Leinonen; V. Peltola; A. Ruohola; O. Ruuskanen
Chronic forms of viral B,C and D hepatitis and fulminant hepatitis represent a serious healthcare problem. The study deals with the changes in the strategy in treating these diseases. During the chronic active hepatitis caused by the B hepatitis virus, the main aim of treatment is to cease multiplication of viruses, eliminate the clinical symptoms, prevent the development of cirrhosis, or the origin of hepatocellular carcinoma. The authors analyze the possibilities of the application of corticosteroids, viricidal drugs (vidarabin and interferons) and other medicaments (acyclovir, zidovudin, duramin, gancyclovir, chinacrin, and others) besides corticosteroids, interleukin 2 and tymozin from the group of immunomodulators were tested. The testing included the factor stimulating the colonies of granulocytes and myeloblasts and other substances. The therapy of acute protracted B hepatitis by means of interferon still requires controlled studies. Superinfection by D virus in chronic carriers of HBsAG causes chronic hepatitis which quickly leads to the development of cirrhosis. The therapy on basis of alpha interferon decreases the RNA virus D hepatitis serum level and leads to an improvement in the development of chronic hepatitis in half of the patients. Therapy of chronic C hepatitis on basis of corticosteroids is ineffective, and can be dangerous. Acyclovir is proved to be ineffective as well. The open study indicated certain positive results in application of interferon. The fulminant hepatitis can be defined as a development of encephalopathy and a decrease of the prothrombin time to less than 50% in the course of acute hepatitis. The break-point in the therapy of fulminant hepatitis took place in association with the performance of the transplantation of the liver. Impossibility to transplant the liver means that the effect of therapy of fulminant hepatitis is merely of supportive value. Majority of patients die due to neurologic complications, namely unmanageable oedema of the brain. But still, neither the antioedema therapy, e.g. on basis of manitol, as well as by means of corticosteroids, hemodialysis, hemofiltration, plasmapheresis and hemoperfusion, nor the treatment on basis of E1 prostaglandine improved the survival of patients. (Tab. 2, Ref. 82). PMID:8556359
Miguet, J; Hrusovský, S
Gene therapy has become a promising strategy for the treatment of many inheritable or acquired diseases that are currently considered incurable. Non-viral vectors have attracted great interest, as they are simple to prepare, rather stable, easy to modify and relatively safe, compared to viral vectors. Unfortunately, they also suffer from a lower transfection efficiency, requiring additional effort for their optimization. The cationic polymer polyethylenimine (PEI) has been widely used for non-viral transfection in vitro and in vivo and has an advantage over other polycations in that it combines strong DNA compaction capacity with an intrinsic endosomolytic activity. Here, we give some insight into strategies developed for PEI-based non-viral vectors to overcome intracellular obstacles, including the improvement of methods for polyplex preparation and the incorporation of endosomolytic agents or nuclear localization signals. In recent years, PEI-based non-viral vectors have been locally or systemically delivered, mostly to target gene delivery to tumor tissue, the lung or liver. This requires strategies to efficiently shield transfection polyplexes against non-specific interaction with blood components, extracellular matrix and untargeted cells and the attachment of targeting moieties, which allow for the directed gene delivery to the desired cell or tissue. In this context, materials, facilitating the design of novel PEI-based non-viral vectors are described. PMID:15939236
Lungwitz, U; Breunig, M; Blunk, T; Göpferich, A
Background: Vaccines have a major role in eradication programs of viral diseases. Vaccines against measles, rubella, and varicella are included in the vaccination schedules for children in most countries. Objective: A comparative analysis between 2011 and 2012 was performed to investigate if the number of patients with viral exanthemas reported to our clinic in 2012 was increased. Materials and Methods: Patients were grouped in four categories: rubella, measles, varicella and other viral exanthemas. Results: Between January and April 2011, there were registered 37 cases with viral exanthemas: 69.5% presented with varicella and 30.5% with other viral exanthemas. Between January and April 2012, there were 178 cases registered with viral eruption, of which 37% were of other viral exanthemas, 35.4% rubella, 19.7% measles and 7.9% varicella. The highest incidence was seen in patients aged between 20 and 29 years (52.2%), with 21% having measles, 32.2% rubella, 9% varicella and 37.6% having other exanthemas. In 2012, the number of cases of viral exanthemas increased 5 times, with important outbreaks of new cases of measles and rubella. Conclusions: Although vaccines against measles and rubella were being used since 1979 and 1998 respectively, it was only in 2004, that these vaccines became part of the mandatory vaccination schedule. Although persons under 32 years should be protected against measles infection if they are previously vaccinated, more than 90% of the registered cases of measles occurred in such patients. The patients registered between January and April 2011 were mostly pediatric. Adults also were much more affected with measles, rubella, or varicella viruses in 2012 than in 2011.
Salavastru, Carmen Maria; Stanciu, Anca Mihaela; Fritz, Klaus; Tiplica, George Sorin
RNA-Based Immunity Terminates Viral Infection in Adult Drosophila in the Absence of Viral Suppression of RNA Interference: Characterization of Viral Small Interfering RNA Populations in Wild-Type and Mutant Flies?‡
Replication of viral RNA genomes in fruit flies and mosquitoes induces the production of virus-derived small interfering RNAs (siRNAs) to specifically reduce virus accumulation by RNA interference (RNAi). However, it is unknown whether the RNA-based antiviral immunity (RVI) is sufficiently potent to terminate infection in adult insects as occurs in cell culture. We show here that, in contrast to robust infection by Flock house virus (FHV), infection with an FHV mutant (FHV?B2) unable to express its RNAi suppressor protein B2 was rapidly terminated in adult flies. FHV?B2 replicated to high levels and induced high mortality rates in dicer-2 and argonaute-2 mutant flies that are RNAi defective, demonstrating that successful infection of adult Drosophila requires a virus-encoded activity to suppress RVI. Drosophila RVI may depend on the RNAi activity of viral siRNAs since efficient FHV?B2 infection occurred in argonaute-2 and r2d2 mutant flies despite massive production of viral siRNAs. However, RVI appears to be insensitive to the relative abundance of viral siRNAs since FHV?B2 infection was terminated in flies carrying a partial loss-of-function mutation in loquacious required for viral siRNA biogenesis. Deep sequencing revealed a low-abundance population of Dicer-2-dependent viral siRNAs accompanying FHV?B2 infection arrest in RVI-competent flies that included an approximately equal ratio of positive and negative strands. Surprisingly, viral small RNAs became strongly biased for positive strands at later stages of infection in RVI-compromised flies due to genetic or viral suppression of RNAi. We propose that degradation of the asymmetrically produced viral positive-strand RNAs associated with abundant virus accumulation contributes to the positive-strand bias of viral small RNAs.
Han, Yan-Hong; Luo, Ying-Jun; Wu, Qingfa; Jovel, Juan; Wang, Xiao-Hong; Aliyari, Roghiyh; Han, Chenggui; Li, Wan-Xiang; Ding, Shou-Wei
Gene delivery is one of the biggest challenges in the field of gene therapy. It involves the efficient transfer of transgenes into somatic cells for therapeutic purposes. A few major drawbacks in gene delivery include inefficient gene transfer and lack of sustained transgene expression. However, the classical method of using viral vectors for gene transfer has circumvented some of these issues. Several kinds of viruses, including retrovirus, adenovirus, adeno-associated virus, and herpes simplex virus, have been manipulated for use in gene transfer and gene therapy applications. The transfer of genetic material into lacrimal epithelial cells and tissues, both in vitro and in vivo, has been critical for the study of tear secretory mechanisms and autoimmunity of the lacrimal gland. These studies will help in the development of therapeutic interventions for autoimmune disorders such as Sjögren’s syndrome and dry eye syndromes which are associated with lacrimal dysfunction. These studies are also critical for future endeavors which utilize the lacrimal gland as a reservoir for the production of therapeutic factors which can be released in tears, providing treatment for diseases of the cornea and posterior segment. This review will discuss the developments related to gene delivery and gene therapy in the lacrimal gland using several viral vector systems.
Selvam, Shivaram; Thomas, Padmaja B.; Hamm-Alvarez, Sarah F.; Schechter, Joel E.; Stevenson, Douglas; Mircheff, Austin K.; Trousdale*, Melvin D.
The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate.
Chan, Joseph Minhow; Carlsson, Gunnar; Rabadan, Raul
NASA Langley Research Center has successfully developed an electron beam freeform fabrication (EBF3) process, a rapid metal deposition process that works efficiently with a variety of weldable alloys. The EBF3 process can be used to build a complex, unitized part in a layer-additive fashion, although the more immediate payoff is for use as a manufacturing process for adding details to components fabricated from simplified castings and forgings or plate products. The EBF3 process produces structural metallic parts with strengths comparable to that of wrought product forms and has been demonstrated on aluminum, titanium, and nickel-based alloys to date. The EBF3 process introduces metal wire feedstock into a molten pool that is created and sustained using a focused electron beam in a vacuum environment. Operation in a vacuum ensures a clean process environment and eliminates the need for a consumable shield gas. Advanced metal manufacturing methods such as EBF3 are being explored for fabrication and repair of aerospace structures, offering potential for improvements in cost, weight, and performance to enhance mission success for aircraft, launch vehicles, and spacecraft. Near-term applications of the EBF3 process are most likely to be implemented for cost reduction and lead time reduction through addition of details onto simplified preforms (casting or forging). This is particularly attractive for components with protruding details that would require a significantly large volume of material to be machined away from an oversized forging, offering significant reductions to the buy-to-fly ratio. Future far-term applications promise improved structural efficiency through reduced weight and improved performance by exploiting the layer-additive nature of the EBF3 process to fabricate tailored unitized structures with functionally graded microstructures and compositions.
Glaessgen, Edward H.; Schoeppner, Gregory A.
We aimed at evaluating the relationship between microbial, etiology and chest radiograph appearance in various types of pneumonia. In a prospective study, the radiographic findings in 479 cases of acute pneumonia in children were compared with viral etiology and growth of potential bacterial pathogens in nasopharyngeal secretion. As the basis for viral etiology was most conclusive, the material was here
H. Wahlgren; W. Mortensson; M. Eriksson; Y. Finkel; M. Forsgren
Antibodies have the potential to be immunotherapeutic agents, used either as stand-alone therapy or as an adjunct for managing chronic viral infection. In addition, antibodies may be used prophylactically in individuals who have been accidentally exposed to hepatitis B virus (HBV) or hepatitis C virus (HCV), or to prevent re-infection of the liver in patients who have undergone liver transplantation. Human monoclonal antibodies to HBV and HCV were generated and their ability to reduce viral load was tested in different animal model systems, the Trimera mouse model and HBV-carrier chimpanzees. These antibodies were further developed and are currently being studied in clinical trials for chronic HBV or HCV and in liver transplant patients. The antibodies were shown to be safe, tolerable and could significantly reduce viral load. Their ability to inhibit HCV re-infection in the transplanted liver is being evaluated. PMID:12772504
Dagan, Shlomo; Eren, Rachel
Viral infections are an important complication of transplantation. The introduction of more potent immunosuppressive agents over the past decade correlates with an increase in the rate of hospitalizations of transplant patients with infections. Specifically, viral infections have emerged as a major source of morbidity and mortality in transplantation. There are several potential intervention strategies in the face of emerging infections and it is likely that the approach will differ depending on the virus in question. These include viral surveillance and pre-emptive therapy, intervention of the transplant community, and policy change at the level of government, blood bank and organ procurement organizations. This review focuses on the emergence of the herpesviruses; HHV-6 and HHV-7. In addition, the issue of virus transmission through organ transplant is addressed with a discussion of West Nile virus and the rabies virus. PMID:17032433
Smith, Jodi M; McDonald, Ruth A
SUMMARY Like their host cells, many viruses produce noncoding (nc)RNAs. These show diversity with respect to time of expression during viral infection, length and structure, protein-binding partners and relative abundance compared with their host-cell counterparts. Viruses, with their limited genomic capacity, presumably evolve or acquire ncRNAs only if they selectively enhance the viral life cycle or assist the virus in combating the host’s response to infection. Despite much effort, identifying the functions of viral ncRNAs has been extremely challenging. Recent technical advances and enhanced understanding of host-cell ncRNAs promise accelerated insights into the RNA warfare mounted by this fascinating class of RNPs.
Steitz, Joan; Borah, Sumit; Cazalla, Demian; Fok, Victor; Lytle, Robin; Mitton-Fry, Rachel; Riley, Kasandra; Samji, Tasleem
In this review we want to consider some of the requirements for autoimmune disease to develop and how this may be reproduced in animal models. Besides a genetic predisposition, environmental triggering factors seem to play a central role in the etiology of many autoimmune diseases. In theory, a structural similarity or identity between the host and an invading pathogen might cause the immune system of the host to react not only to the pathogen but also to self-components. However, in order for such a process of molecular mimicry to induce autoimmunity the mechanisms of maintaining tolerance or ignorance to the self-components need to be circumvented. Subsequently, in order to advance autoimmunity to overt autoimmune disease the frequency and avidity of autoaggressive lymphocytes has to be of sufficient magnitude. Intuitively, one would assume that tolerance might be stronger to identical structures than to structures that just share a certain degree of similarity. Self-reactive lymphocytes with high-avidity are more likely to be deleted or functionally silenced by central and/or peripheral tolerance mechanisms. Thus, perfect mimicry between identical structures might fail in inducing autoimmunity because of efficient tolerance mechanisms. In contrast, imperfect mimicry between similar but not identical structures might on one hand circumvent tolerance but on the other hand result in the generation of lymphocytes with only low- to intermediate avidity. Here we examine animal models that use the concept of molecular mimicry as a potential mechanism for inducing or accelerating autoimmunity. We focus on the RIP-LCMV model for type 1 diabetes and the novel cytochrome P450 2D6 (CYP2D6) model for autoimmune hepatitis, which use either identical or similar triggering and target antigens.
Christen, Urs; Hintermann, Edith; Holdener, Martin; von Herrath, Matthias G.
Gammaherpesvirus cyclins have expanded biochemical features relative to mammalian cyclins, and promote infection and pathogenesis including acute lung infection, viral persistence, and reactivation from latency. To define the essential features of the viral cyclin, we generated a panel of knock-in viruses expressing various viral or mammalian cyclins from the murine gammaherpesvirus 68 cyclin locus. Viral cyclins of both gammaherpesvirus 68 and Kaposi's sarcoma-associated herpesvirus supported all cyclin-dependent stages of infection, indicating functional conservation. Although mammalian cyclins could not restore lung replication, they did promote viral persistence and reactivation. Strikingly, distinct and non-overlapping mammalian cyclins complemented persistence (cyclin A, E) or reactivation from latency (cyclin D3). Based on these data, unique biochemical features of viral cyclins (e.g. enhanced kinase activation) are not essential to mediate specific processes during infection. What is essential for, and unique to, the viral cyclins is the integration of the activities of several different mammalian cyclins, which allows viral cyclins to mediate multiple, discrete stages of infection. These studies also demonstrated that closely related stages of infection, that are cyclin-dependent, are in fact genetically distinct, and thus predict that cyclin requirements may be used to tailor potential therapies for virus-associated diseases.
Lee, Katherine S.; Suarez, Andrea L.; Claypool, David J.; Armstrong, Taylor K.; Buckingham, Erin M.; van Dyk, Linda F.
Hepatitis C is a pandemic human RNA virus, which commonly causes chronic infection and liver disease. The characterization of viral populations that successfully initiate infection, and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design. A comprehensive and longitudinal analysis of the viral population was conducted in four subjects followed from very early acute infection to resolution of disease outcome. By means of next generation sequencing (NGS) and standard cloning/Sanger sequencing, genetic diversity and viral variants were quantified over the course of the infection at frequencies as low as 0.1%. Phylogenetic analysis of reassembled viral variants revealed acute infection was dominated by two sequential bottleneck events, irrespective of subsequent chronicity or clearance. The first bottleneck was associated with transmission, with one to two viral variants successfully establishing infection. The second occurred approximately 100 days post-infection, and was characterized by a decline in viral diversity. In the two subjects who developed chronic infection, this second bottleneck was followed by the emergence of a new viral population, which evolved from the founder variants via a selective sweep with fixation in a small number of mutated sites. The diversity at sites with non-synonymous mutation was higher in predicted cytotoxic T cell epitopes, suggesting immune-driven evolution. These results provide the first detailed analysis of early within-host evolution of HCV, indicating strong selective forces limit viral evolution in the acute phase of infection.
McElroy, Kerensa; Gaudieri, Silvana; Pham, Son T.; Chopra, Abha; Cameron, Barbara; Maher, Lisa; Dore, Gregory J.; White, Peter A.; Lloyd, Andrew R.
The aetiology of obesity is multifactorial. An understanding of the contributions of various causal factors is essential for the proper management of obesity. Although it is primarily thought of as a condition brought on by lifestyle choices, recent evidence shows there is a link between obesity and viral infections. Numerous animal models have documented an increased body weight and a number of physiologic changes, including increased insulin sensitivity, increased glucose uptake and decreased leptin secretion that contribute to an increase in body fat in adenovirus-36 infection. Other viral agents associated with increasing obesity in animals included canine distemper virus, rous-associated virus 7, scrapie, Borna disease virus, SMAM-1 and other adenoviruses. This review attempted to determine if viral infection is a possible cause of obesity. Also, this paper discussed mechanisms by which viruses might produce obesity. Based on the evidence presented in this paper, it can be concluded that a link between obesity and viral infections cannot be ruled out. Further epidemiologic studies are needed to establish a causal link between the two, and determine if these results can be used in future management and prevention of obesity. PMID:19874530
Mitra, A K; Clarke, K
This article reviews the current state of knowledge on the viral haemorrhagic fevers that infect man, namely smallpox, chikungunya fever, dengue fever, Rift Valley fever, yellow fever, Crimean haemorrhagic fever, Kyasanur Forest disease, Omsk haemorrhagic fever, Argentinian haemorrhagic fever (Junin virus), Bolivian haemorrhagic fever (Machupo virus), Lassa fever, haemorrhagic fever with renal syndrome, and Marburg and Ebola virus diseases.
Simpson, D. I. H.
Dengue viral infections affect up to 100 million individuals per year. Dengue haemorrhagic fever is a clinical form of disease characterised by intravascular fluid loss. There has been a marked increase in the incidence of this form of the disease over the last few decades, associated with significant mortality, particularly in the paediatric population. A number of theories relating to
William J. H McBride; Helle Bielefeldt-Ohmann
Viral Marketing, the idea of exploiting social interactions of users to propagate awareness for products, has gained considerable focus in recent years. One of the key issues in this area is to select the best seeds that maximize the influence propagated in the social network. In this paper, we define the seed selection problem (called t-Influence Maximization, or t-IM) for
Samik Datta; Anirban Majumder; Nisheeth Shrivastava
To date cancer vaccines have yet to show efficacy in a phase III trial. However, the clinical benefit seen with monoclonal antibody mediated therapies (e.g., Herceptin) has provided proof of principle that immune responses directed against tumour-associated antigens could have therapeutic potential. The failure of past cancer vaccine trials is likely due to several factors including the inappropriate choice of tumour antigen, use of an unoptimised antigen delivery system or vaccination schedule or selection of the wrong patient group. Any one of these variables could potentially result in the induction of an immune response of insufficient magnitude to deliver clinical benefit. Live recombinant viral vaccines have been used in the development of cancer immunotherapy approaches for the past 10 years. Though such vectors are self-adjuvanted and offer the ability to express multiple tumour-associated antigens (TAAs) along with an array of immune co-factors, arguably, they have yet to demonstrate convincing efficacy in pivotal clinical trials. However, in recent years, more coordinated studies have revealed mechanisms to optimise current vectors and have lead to the development of new advantageous vector systems. In this review, we highlight that live recombinant viral vectors provide a versatile and effective antigen delivery system and describe the optimal properties of an effective viral vector. Additionally, we discuss the advantages and disadvantages of the panel of recombinant viral systems currently available to cancer vaccinologists and how they can work in synergy in heterologous prime boost protocols and with other treatment modalities. PMID:17030074
Harrop, Richard; John, Justin; Carroll, Miles W
Viruses are important causes of nosocomial infection, but the fact that hospital outbreaks often result from introduction(s) from community-based epidemics, together with the need to initiate specific laboratory testing, means that there are usually insufficient data to allow the monitoring of trends in incidences. The most important defenses against nosocomial transmission of viruses are detailed and continuing education of staff and strict adherence to infection control policies. Protocols must be available to assist in the management of patients with suspected or confirmed viral infection in the health care setting. In this review, we present details on general measures to prevent the spread of viral infection in hospitals and other health care environments. These include principles of accommodation of infected patients and approaches to good hygiene and patient management. They provide detail on individual viral diseases accompanied in each case with specific information on control of the infection and, where appropriate, details of preventive and therapeutic measures. The important areas of nosocomial infection due to blood-borne viruses have been extensively reviewed previously and are summarized here briefly, with citation of selected review articles. Human prion diseases, which present management problems very different from those of viral infection, are not included.
Aitken, Celia; Jeffries, Donald J.
A study of the incidence and etiology (viral and mycoplasmal) of croup, bronchiolitis and pneumonia was initiated. The study group is a population of nearly 8,000 children 5 years and under. Two hundred and eighteen cases were recorded in the first 2 1/2 ...
J. T. Grayston
The use of preimplantation genetic diagnosis (PGD) has expanded both in number and scope over the past 2 decades. Initially carried out to avoid the birth of children with severe genetic disease, PGD is now used for a variety of medical and non-medical purposes. While some human studies have concluded that PGD is safe, animal studies and a recent human study suggest that the embryo biopsy procedure may result in neurological problems for the offspring. Given that the long-term safety of PGD has not been clearly established in humans, this study sought to determine how PGD safety is presented to prospective patients by means of a detailed website analysis. The websites of 262 US fertility centres performing PGD were analysed and comments about safety and risk were catalogued. Results of the analysis demonstrated that 78.2% of centre websites did not mention safety or risk of PGD at all. Of the 21.8% of centres that did contain safety or risk information about PGD, 28.1% included statements highlighting the potential risks, 38.6% presented information touting the procedure as safe and 33.3% included statements highlighting potential risks and the overall safety of the procedure. Thus, 86.6% of PGD-performing centres state that PGD is safe and/or fail to disclose any risks on their websites despite the fact that the impact of the procedure on the long-term health of offspring is unproven. This lack of disclosure suggests that informed consent is inadequate; this study examines numerous factors that are likely to inhibit comprehensive discussions of safety. PMID:22493184
LaBonte, Michelle Lynne
The Discovery Education website serves as a repository of instructional materials for educators seeking to help their charges learn about everything from the solar system to genetically modified organisms. This particular lesson plan deals with the science and technology of genetic engineering and it is intended to be used by advanced high school and community college students. Users will appreciate the fact that the entire plan is well-organized and divided into 12 sections including Objectives, Discussion Questions, and Procedures. The Discussion Questions are thoughtful and well-articulated and one can imagine that each query might generate more than a bit of meditation and close consideration.
The three types of interferon (IFNs) are essential for immunity against at least some viruses in the mouse model of experimental infections, type I IFNs displaying the broadest and strongest anti-viral activity. Consistently, human genetic studies have shown that type II IFN is largely redundant for immunity against viruses in the course of natural infections. The precise contributions of human type I and III IFNs remain undefined. However, various inborn errors of anti-viral IFN immunity have been described, which can result in either broad or narrow immunological and viral phenotypes. The broad disorders impair the response to (STAT1, TYK2) or the production of at least type I and type III IFNs following multiple stimuli (NEMO), resulting in multiple viral infections at various sites, including herpes simplex encephalitis (HSE). The narrow disorders impair exclusively (TLR3) or mostly (UNC-93B, TRIF, TRAF3) the TLR3-dependent induction of type I and III IFNs, leading to HSE in apparently otherwise healthy individuals. These recent discoveries highlight the importance of human type I and III IFNs in protective immunity against viruses, including the TLR3-IFN pathway in protection against HSE.
Sancho-Shimizu, Vanessa; de Diego, Rebeca Perez; Jouanguy, Emmanuelle; Zhang, Shen-Ying; Casanova, Jean-Laurent
Background Herbal medicines are being used for treating viral diseases including viral myocarditis, and many controlled trials have been done to investigate their efficacy. Objectives To assess the effects of herbal medicines on clinical and indirect outcomes in patients with viral myocarditis. Search methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library Issue 3, 2009, MEDLINE (January 1966 - July 2009), EMBASE (January 1998 - July 2009), Chinese Biomedical Database (1979 - 2009), China National Knowledge Infrastructure (1979 - 2009), Chinese VIP Information (1989 - 2009), Chinese Academic Conference Papers Database and Chinese Dissertation Database (1980 - 2009), AMED (1985 - 2009), LILACS accessed in July 2009 and the trials register of the Cochrane Complementary Medicine Field. We handsearched Chinese journals and conference proceedings. No language restrictions were applied. Selection criteria Randomised controlled trials of herbal medicines (with a minimum of seven days treatment duration) compared with placebo, no intervention, or conventional interventions were included. Trials of herbal medicine plus conventional drug versus drug alone were also included. Only trials that reported adequate description of allocation sequence generation were included. Data collection and analysis Two review authors independently extracted data and evaluated trial quality. Adverse effects information was collected from the trials. Results Fourteen randomised trials involving 1463 people were included. All trials were conducted and published in China. Quality of the trials was assessed to be low. No trial had diagnosis of viral myocarditis confirmed histologically, and only a few trials attempted to establish viral aetiology. Nine different herbal medicines were tested in the included trials. The trials reported electrocardiogram results, level of myocardial enzymes, cardiac function, symptoms, and adverse effects. Astragalus membranaceus (either as an injection or granules) showed significant positive effects in symptom improvement, normalisation of electrocardiogram results, CPK levels, and cardiac function. Shengmai injection also showed significant effects in symptom improvement. Shengmai decoction triggered significant improvement in quality of life measured by SF-36. No serious adverse effects were reported. Authors' conclusions Some herbal medicines may lead to improvement of symptoms, ventricular premature beat, electrocardiogram, level of myocardial enzymes, and cardiac function in viral myocarditis. However, interpretation of these findings should be taken with care due to the low methodological quality, small sample size, and limited number of trials on individual herbs. Further robust trials are needed to explore the use of herbal medicines in viral myocarditis.
Liu, Zhao Lan; Liu, Zhi Jun; Liu, Jian Ping; Yang, Min; Kwong, Joey
Background Herbal medicines are being used for treating viral diseases including viral myocarditis, and many controlled trials have been done to investigate their efficacy. Objectives To assess the effects of herbal medicines on clinical and indirect outcomes in patients with viral myocarditis. Search strategy We searched the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library Issue 3, 2009, MEDLINE (January 1966 - July 2009), EMBASE (January 1998 - July 2009), Chinese Biomedical Database (1979 - 2009), China National Knowledge Infrastructure (1979 - 2009), Chinese VIP Information (1989 - 2009), Chinese Academic Conference Papers Database and Chinese Dissertation Database (1980 - 2009), AMED (1985 - 2009), LILACS accessed in July 2009 and the trials register of the Cochrane Complementary Medicine Field. We handsearched Chinese journals and conference proceedings. No language restrictions were applied. Selection criteria Randomised controlled trials of herbal medicines (with a minimum of seven days treatment duration) compared with placebo, no intervention, or conventional interventions were included. Trials of herbal medicine plus conventional drug versus drug alone were also included. Only trials that reported adequate description of allocation sequence generation were included. Data collection and analysis Two review authors independently extracted data and evaluated trial quality. Adverse effects information was collected from the trials. Main results Fourteen randomised trials involving 1463 people were included. All trials were conducted and published in China. Quality of the trials was assessed to be low. No trial had diagnosis of viral myocarditis confirmed histologically, and only a few trials attempted to establish viral aetiology. Nine different herbal medicines were tested in the included trials. The trials reported electrocardiogram results, level of myocardial enzymes, cardiac function, symptoms, and adverse effects. Astragalus membranaceus (either as an injection or granules) showed significant positive effects in symptom improvement, normalisation of electrocardiogram results, CPK levels, and cardiac function. Shengmai injection also showed significant effects in symptom improvement. Shengmai decoction triggered significant improvement in quality of life measured by SF-36. No serious adverse effects were reported. Authors’ conclusions Some herbal medicines may lead to improvement of symptoms, ventricular premature beat, electrocardiogram, level of myocardial enzymes, and cardiac function in viral myocarditis. However, interpretation of these findings should be taken with care due to the low methodological quality, small sample size, and limited number of trials on individual herbs. Further robust trials are needed to explore the use of herbal medicines in viral myocarditis.
Liu, Zhao Lan; Liu, Zhi Jun; Liu, Jian Ping; Yang, Min; Kwong, Joey
This book begins with an overview of the current principles of genetics and molecular genetics. Over this foundation, it adds detailed and specialized information: a description of the translation, transcription, expression and regulation of DNA and RNA; a description of the manipulation of genetic material via promoters, enhancers, and gene splicing; and a description of cloning techniques, especially those for blood group genes. The last chapter looks to the impact of molecular genetics on transfusion medicine.
Viruses are the simplest ``life'' form. These parasites reproduce by borrowing the machinery of their host cell. Many are pathogenic to plants, animals, and humans. Viruses possess an outer protein coat (capsid) that protects its genomic material that resides inside. We have developed a theoretical technique to model the very low frequency mechanical modes of the viral capsid with atomic resolution. The method uses empirical force fields and a mathematical framework borrowed from electronic structure theory for finding low energy states. The low frequency modes can be ``pinged'' with an ultra-short laser pulse and the aim of the light/vibrational coupling is to interfere with the viral life cycle. The theoretical work here is motivated by the recent work of Tsen et al.  who have used ultra-short pulsed laser scattering to inactivate viruses. The methodology can be applied to many systems, and the coupled mechanical oscillations of other floppy biomolecules such as a complete ATP binding cassette (ABC transporter) will also be discussed. Co-authors of this work are Dr. Eric Dykeman, Prof. K.-T. Tsen and Daryn Benson. [4pt]  E.C. Dykeman et al., Phys. Rev. Lett., 100, 028101 (2008). [0pt]  K-T. Tsen et al., J. of Physics -- Cond. Mat. 19, 472201 (2007).
Sankey, Otto F.
The Orchidaceae is one of the most famous garden plants, and improvement of the orchid is very important in horticulture field. However, molecular information is largely unknown. We found a Phalaenopsis variety harboring floral organs showing C class homeotic change. Column is composed of the anthers with the receptive stigmatic surface just underneath them in wild type. However the C class variety produced column with sepal or petal like structure at the abaxial side. This is the typical abnormality as C class mutants in plants. Further, wild type looking revertant was found from the meristem tissue cultured population. This result strongly indicates the existence of active transposable element in Phalaenopsis genome. This transposon may enable Phalaenopsis as a good material for molecular genetic analysis in Orchidaceae. PMID:21670548
Ejima, Chika; Kobayashi, Yuuki; Honda, Hiroaki; Shimizu, Noriko; Kiyohara, Shunsuke; Hamasaki, Ryota; Sawa, Shinichiro
Purpose – There has been little evidence of any work undertaken to measure the effectiveness of viral marketing campaigns. This paper aims to report on research undertaken to determine the key criteria that viral marketing practitioners believe should be used to measure the success of viral marketing campaigns. Design\\/methodology\\/approach – Semi-structured interviews were undertaken with some of the premier web
Danilo Cruz; Chris Fill
The purpose of these studies was to describe procedures employed in studies on the role of viral aerosols in human viral respiratory disease. The results showed that viral aerosols prepared with the Collison atomizer can be adjusted to a desired content o...
P. J. Gerone R. B. Couch G. V. Keefer R. G. Douglas E. B. Derrenbacher
Infection by RNA viruses is followed by the appearance of viral RNA in cells. As well as single and double stranded forms of the viral RNA another viral specific RNA can be found in chicken embryo fibroblast cells infected with the arbovirus Semliki forest virus. This may be concerned in the production of protein specific to this virus.
J. A. Sonnabend; E. M. Martin; E. Mécs
We demonstrate rapid microfluidic fabrication of hybrid microparticles composed of functionalized viral nanotemplates directly embedded in polymeric hydrogels. Specifically, genetically modified tobacco mosaic virus (TMV) templates were covalently labeled with fluorescent markers or metalized with palladium (Pd) nanoparticles (Pd-TMV), then suspended in a poly(ethylene glycol)-based solution. Upon formation in a flow-focusing device, droplets were photopolymerized with UV light to form microparticles. Fluorescence and confocal microscopy images of microparticles containing fluorescently labeled TMV show uniform distribution of TMV nanotemplates throughout the microparticles. Catalytic activity, via the dichromate reduction reaction, is also demonstrated with microparticles containing Pd-TMV complexes. Additionally, Janus microparticles were fabricated containing viruses embedded in one side and magnetic nanoparticles in the other, that enabled simple separation from bulk solution. These results represent a facile route to directly harness the advantages of viral nanotemplates into a readily usable and stable 3D assembled format.
Lewis, Christina L.; Lin, Yan; Yang, Cuixian; Manocchi, Amy K.; Yuet, Kai P.; Doyle, Patrick S.; Yi, Hyunmin
Viral exanthems are a common problem in tropical regions, particularly affecting children. Most exanthems are transient and harmless, but some are potentially very dangerous. Pregnant women and malnourished or immunocompromised infants carry the greatest risk of adverse outcome. In this article, parvovirus B19; dengue and yellow fever; West Nile, Barmah Forest, Marburg, and Ebola viruses, and human herpesviruses; asymmetric periflexural exanthema of childhood; measles; rubella; enteroviruses; Lassa fever; and South American hemorrhagic fevers will be discussed. PMID:17350501
Carneiro, Sueli Coelho da Silva; Cestari, Tania; Allen, Samuel H; Ramos e-Silva, Marcia
ABSTRACT Global competition on the Internet marketplace requires thorough planning and careful investment of capital. Start-up companies,with a limited budget need to reduce cost wherever feasible. Eliminating license costs by using Open Source Software is a big saving for a company,and viral marketing has become,the number,one option to dynamically create brand awareness. The power of online influence, namely, „word of
Chromatin remodeling and gene expression are regulated by histone deacetylases (HDACs) that condense the chromatin structure\\u000a by deacetylating histones. HDACs comprise a group of enzymes that are responsible for the regulation of both cellular and\\u000a viral genes at the transcriptional level. In mammals, a total of 18 HDACs have been identified and grouped into four classes,\\u000a i.e., class I (HDACs
Georges Herbein; Daniel Wendling
The capacity of different bovine viral diarrhea virus (BVDV) strains to cause transplacental infection is variable. BVDV strain SD-1 was isolated from a persistently infected heifer. Its genome represents the only reported nucleotide sequence of a noncytopathic viral isolate determined without cell culture passage in the laboratory. Thus, SD-1 might possess biological advantages over other NCP BVDV strains to be used as a model virus for investigation of viral transplacental transmission. To evaluate if a molecularly generated BVDV SD-1 is capable of crossing the bovine placenta efficiently, a full-length cDNA clone of SD-1 was constructed using RT-PCR amplification and standard molecular techniques. In vitro transcripts synthesized from the cDNA template directed the generation of infectious virus in MDBK cells with a transfection efficiency as high as 4.7 x 10(5) FFU/mug RNA. The recovered virus termed ASD1 harbored five silent point mutations engineered as genetic markers and was similar to wild type (wt) SD-1 in viral growth kinetics. As evaluated in the pregnant heifers, ASD1 was capable of crossing the bovine placenta efficiently, suggesting that NCP BVDV SD-1 is a suitable viral backbone for investigation of the role of viral genetic element(s) in viral transplacental transmission by allowing for evaluation of newly created viral mutants. PMID:19067148
Fan, Zhen-Chuan; Wang, Hai-Hong
Viruses can be engineered to efficiently deliver exogenous genes, but their natural gene delivery properties often fail to meet human therapeutic needs. Therefore, engineering viral vectors with new properties, including enhanced targeting abilities and resistance to immune responses, is a growing area of research. This review discusses protein engineering approaches to generate viral vectors with novel gene delivery capabilities. Rational design of viral vectors has yielded successful advances in vitro, and to an extent in vivo. However, there is often insufficient knowledge of viral structure-function relationships to reengineer existing functions or create new capabilities, such as virus-cell interactions, whose molecular basis is distributed throughout the primary sequence of the viral proteins. Therefore, high-throughput library and directed evolution methods offer alternative approaches to engineer viral vectors with desired properties. Parallel and integrated efforts in rational and library-based design promise to aid the translation of engineered viral vectors toward the clinic.
Schaffer, David V.; Koerber, James T.; Lim, Kwang-il
The authors presented the results of DNA polymorphism investigation of blood, buccal swabs and hair follicles originating from patients after allogeneic hematopoietic stem cell transplantation. The real-time and multiplex assays based on polymerase chain reaction within the range of autosomal as well as Y-chromosomal markers were applied to assess the possible dangers arising from investigation of these materials in forensic genetics. The results revealed that not only post-transplant blood and buccal swab, but also recipient hair, up to now regarded as devoid of any donor's cells, do not constitute entirely safe material for forensic purposes. Their analysis can lead to the false identification of gender or male haplotype. The investigation of sex-determining region Y and Y-chromosome short tandem repeats performed in female recipients with male donors resulted in the designation of donor's DNA in hair cells as well as in blood and buccal swabs. Therefore, biological stains gathered from crime scenes should not be analysed exclusively based on the investigation of male-specific markers. PMID:23052441
Jacewicz, Renata; Lewandowski, Krzysztof; Rupa-Matysek, Joanna; Jedrzejczyk, Maciej; Komarnicki, Mieczys?aw; Berent, Jaros?aw
There are more than 160 viral species in the Rhabdovidae family, most of which can be grouped into one of the six genera including Vesiculovirus, Lyssavirus, Ephemerovirus, Novirhabdovirus, Cytorhabdovirus, and Nucleorhabdovirus. These viruses are not only morphologically similar but also genetically related. Analysis of viral genes shows that rhabdoviruses are more closely related to each other than to viruses in
Z. F. Fu
The Maine Science Corps is a project sponsored by the National Science Foundation's (NSF) Graduate Teaching Fellows in K-12 Education (GK-12 ) program. Through this program, the University of Southern Maine's (USM) virology and transmission electron microscopy (TEM) research group provides high school teachers and students in rural areas with…
Duboise, S. Monroe; Moulton, Karen D.; Jamison, Jennifer L.
The complex structure of virus populations has been the object of intensive study in bacteria, animals, and plants for over a decade. While it is clear that tremendous genetic diversity is rapidly generated during viral replication, the distribution of this diversity within a single host remains an obscure area in this field of science. Among animal viruses, only Human immunodeficiency
Chiraz Jridi; Jean-Francois Martin; Veronique Marie-Jeanne; Gerard Labonne; Stephane Blanc
Detection, genetic characterization, and control of bovine viral diarrhea virus (BVDV) disease in a large commercial dairy herd is reported. Precolostral BVDV serum antibody was detected in 5.3% (12/226) of newborn calves before the test and removal of persistently infected (PI) animals and in 0.4% (2/450) of newborn calves after the removal of PI heifers.
Schefers, Jeremy M.; Collins, James E.; Goyal, Sagar M.; Ames, Trevor R.
Nodavirus are the causative agents of viral nervous necrosis (VNN), and has been shown to cause mortality in numerous fish species worldwide, among them is the Atlantic cod (Gadus morhua L.). In this study, heritability of VNN resistance in Atlantic cod was estimated through challenge testing of 50 large full sib families (?94 fish per family) comprising two genetically distinct
Jørgen Ødegård; Ann-Inger Sommer; Anne Kettunen Præbel
Rift Valley fever viral strains or variants (RVFV) were compared with respect to (a) virulence for Wistar-Furth rats; (b) in vitro sensitivity to rat and human interferon; (c) ability to form plaques in primary hepatocyte cultures from genetically resista...
G. W. Anderson C. J. Peters
Meaningful advances have been made in understanding the mechanisms that contribute to dilated cardiomyopathy and myocarditis. Our data confirmed the hypothesis that there is an interaction of genetic predisposition and acquired factors, in that both can affect the dystrophin-glycoprotein complex. We could show that dystrophin deficiency increases susceptibility to viral infection. Our experiments addressed the role of coxsackievirus in the
K. U. Knowlton
Cerebral vasospasm (CV) is a major source of morbidity and mortality in aneurysmal subarachnoid hemorrhage (aSAH). It is thought that an inflammatory cascade initiated by extravasated blood products precipitates CV, disrupting vascular smooth muscle cell function of major cerebral arteries, leading to vasoconstriction. Mechanisms of CV and modes of therapy are an active area of research. Understanding the genetic basis of CV holds promise for the recognition and treatment for this devastating neurovascular event. In our review, we summarize the most recent research involving key areas within the genetics and vasospasm discussion: (1) Prognostic role of genetics—risk stratification based on gene sequencing, biomarkers, and polymorphisms; (2) Signaling pathways—pinpointing key inflammatory molecules responsible for downstream cellular signaling and altering these mediators to provide therapeutic benefit; and (3) Gene therapy and gene delivery—using viral vectors or novel protein delivery methods to overexpress protective genes in the vasospasm cascade.
Ladner, Travis R.; Zuckerman, Scott L.; Mocco, J
Describes different sources of readings for understanding issues and concepts of genetic engineering. Broad categories of reading materials are: concerns about genetic engineering; its background; procedures; and social, ethical and legal issues. References are listed. (PS)
Mertens, Thomas R.; Robinson, Sandra K.
NLR proteins are innate immune sensors that respond to microbial infection. Upon pathogen infection, some NLR proteins form large complexes, called inflammasomes, which activate caspase-1 and induce the production of active IL-1? and IL-18. Activation of inflammasomes can also lead to an inflammatory cell death program, named pyroptosis. In this review, we will discuss the role of various NLR proteins in sensing different viral infections, as well as the strategies used by several RNA and DNA viruses to counteract the antiviral effects of NLR-dependent inflammasomes.
Jacobs, Sarah R.; Damania, Blossom
Approximately 40 viruses are known from marine sponges; turbellarian and monogenetic flatworms; cephalopod, bivalve, and gastropod mollusks; nereid polychaetes; and isopod and decapod crustaceans. Most of the viruses can be tentatively assigned to the Herpesviridae, Baculoviridae, Iridoviridae, Adenoviridae, Papovaviridae, Reoviridae, “Birnaviridae”, Bunyaviridae, Rhabdoviridae, and Picornaviridae. Viruslike particles found in oysters might be representatives of the Togaviridae and Retroviridae. Enveloped single-stranded RNA viruses from crustaceans have developmental and morphological characteristics intermediate between families, and some show evidence of relationships to the Paramyxoviridae as well as the Bunyaviridae or Rhabdoviridae. Certain small viruses of shrimp cannot be assigned, even tentatively, to a particular family. Some viruses cause disease in wild and captive hosts, others are associated with disease states but may not be primary instigators, and many occur in apparently normal animals. The frequency of viral disease in natural populations of marine invertebrates is unknown. Several viruses that cause disease in captive animals, with or without experimental intervention, have also been found in diseased wild hosts, including herpeslike viruses of crabs and oysters, iridovirus of octopus, and reolike and bunyalike viruses of crabs. Iridolike viruses have been implicated in massive mortalities of cultured oysters. Baculoviruses, and IHHN virus, which is of uncertain affinities, cause economically damaging diseases in cultured penaeid shrimp. Double or multiple viral infection is common in crabs. For example, a reolike virus and associated rhabdolike virus act synergistically to cause paralytic and fatal disease in Callinectes sapidus. Information on host range, most susceptible stage, and viral latency is available only for viruses of shrimp. One baculovirus attacks five species of New World penaeid shrimp. IHHN virus infects three species of Penaeus and causes catastrophic mortalities in P. stylirostris, but usually exhibits only inapparent infection in P. vannamei. Some shrimp viruses apparently are latent in larvae, causing disease only when shrimp have reached the postlarval or juvenile stages. Others are equally or more pathogenic in larvae. Studies of shrimp viruses and iridovirus-associated disease in cultured oysters point up the need for rapid and accurate diagnostic methods. Until appropriate cell cultures from marine invertebrates are devised, the viral identifications necessary for understanding of epizootiology, rapid containment of epizootics in cultured animals, and decisions regarding introductions of exotic species will be difficult or impossible.
Johnson, P. T.
Are viruses responsible for the pain in patients with fibromyalgia? Are viruses the trigger for rheumatoid arthritis? Is chronic fatigue syndrome a viral disease? There are many open questions with few or controversial answers. According to the current state of knowledge on the origin of the pain in fibromyalgia the varied symptomatic of fibromyalgia is triggered by peripheral as well as central mechanisms. Despite the broad spectrum of symptoms the disease is a specific entity which is mainly treated with dual reuptake inhibitors, anticonvulsives, tramadol, selective serotonin reuptake inhibitors, gamma-hydroxybutyrate and dopamine agonists in individually selected combinations. PMID:21698474
EPA has conditionally registered Syngenta Seeds Inc.'s new active ingredient, modified Cry3A protein and the genetic material necessary for its production (via elements of pZM26) in event MIR604 corn SYN-IR604-8. The Agency has determined that the use of ...
Designed as a high-capacity alloy host for Na-ion chemistry, a forest of Sn nanorods with a unique core-shell structure was synthesized on viral scaffolds, which were genetically engineered to ensure a nearly vertical alignment upon self-assembly onto a metal substrate. The interdigital spaces thus formed between individual rods effectively accommodated the volume expansion and contraction of the alloy upon sodiation/desodiation, while additional carbon-coating engineered over these nanorods further suppressed Sn aggregation during extended electrochemical cycling. Due to the unique nanohierarchy of multiple functional layers, the resultant 3D nanoforest of C/Sn/Ni/TMV1cys, binder-free composite electrode already and evenly assembled on a stainless steel current collector, exhibited supreme capacity utilization and cycling stability toward Na-ion storage and release. An initial capacity of 722 mA·h (g Sn)(-1) along with 405 mA·h (g Sn)(-1) retained after 150 deep cycles demonstrates the longest-cycling nano-Sn anode material for Na-ion batteries reported in the literature to date and marks a significant performance improvement for neat Sn material as alloy host for Na-ion chemistry. PMID:23484633
Liu, Yihang; Xu, Yunhua; Zhu, Yujie; Culver, James N; Lundgren, Cynthia A; Xu, Kang; Wang, Chunsheng
The potato virus X (PVX) virion can be reconstituted in vitro from the virus coat protein (CP) and RNA; heterologous RNAs may be used as well. In our recent study, structure and properties of cognate and heterologous viral ribonucleoproteins (vRNPs) were demonstrated to be similar to those of native virions. The assembly was found to be initiated at the 5' terminus of an RNA and was not dependent on RNA sequence. The aim of the present study was to search for a signal or an essential structural element that directs packaging of viral genetic material into vRNPs. vRNPs were formed by incubation of the PVX CP with heterologous capped RNAs, their functional fragments lacking the cap structure, as well as the capped and uncapped transcripts corresponding to the 5'-terminal region of the genomic PVX RNA. Experimental data show that the presence of the cap structure at the 5' end of a nucleic acid is an important condition for vRNP assembly from RNA and CP. Presumably, the 5'-cap affects conformational state of the RNA region responsible for the efficient interaction with CP and creates conformational encapsidation signal for vRNP assembly. PMID:24036171
Petrova, Ekaterina K; Nikitin, Nikolai A; Protopopova, Anna D; Arkhipenko, Marina V; Yaminsky, Igor V; Karpova, Olga V; Atabekov, Joseph G
Viral capsid proteins assemble into large, symmetrical architectures that are not found in complexes formed by their cellular counterparts. Given the prevalence of the signature jelly-roll topology in viral capsid proteins, we are interested in whether these functionally unique capsid proteins are also structurally unique in terms of folds. To explore this question, we applied a structure-alignment based clustering of all protein chains in VIPERdb filtered at 40% sequence identity to identify distinct capsid folds, and compared the cluster medoids with a non-redundant subset of protein domains in the SCOP database, not including the viral capsid entries. This comparison, using Template Modeling (TM)-score, identified 2078 structural “relatives” of capsid proteins from the non-capsid set, covering altogether 210 folds following the definition in SCOP. The statistical significance of the 210 folds shared by two sets of the same sizes, estimated from 10,000 permutation tests, is less than 0.0001, which is an upper bound on the p-value. We thus conclude that viral capsid proteins are segregated in structural fold space. Our result provides novel insight on how structural folds of capsid proteins, as opposed to their surface chemistry, might be constrained during evolution by requirement of the assembled cage-like architecture. Also importantly, our work highlights a guiding principle for virus-based nanoplatform design in a wide range of biomedical applications and materials science.
Cheng, Shanshan; Brooks, Charles L.
Despite major progress in understanding and managing liver disease in the past 30 years, it is now among the top 10 most common causes of death globally. Several risk factors, such as genetics, diabetes, obesity, excessive alcohol consumption, viral infection, gender, immune dysfunction, and medications, acting individually or in concert, are known to precipitate liver damage. Viral hepatitis, excessive alcohol consumption, and obesity are the major factors causing liver injury. Estimated numbers of hepatitis B virus (HBV) and hepatitis C virus (HCV)-infected subjects worldwide are staggering (370 and 175 million, respectively), and of the 40 million known human immunodeficiency virus positive subjects, 4 and 5 million are coinfected with HBV and HCV, respectively. Alcohol and HCV are the leading causes of end-stage liver disease worldwide and the most common indication for liver transplantation in the United States and Europe. In addition, the global obesity epidemic that affects up to 40 million Americans, and 396 million worldwide, is accompanied by an alarming incidence of end-stage liver disease, a condition exacerbated by alcohol. This article focuses on the interactions between alcohol, viral hepatitis, and obesity (euphemistically described here as the Bermuda Triangle of liver disease), and discusses common mechanisms and synergy. PMID:23855291
Archaeal viruses display unusually high genetic and morphological diversity. Studies of these viruses proved to be instrumental for the expansion of knowledge on viral diversity and evolution. The Sulfolobus islandicus rod-shaped virus 2 (SIRV2) is a model to study virus-host interactions in Archaea. It is a lytic virus that exploits a unique egress mechanism based on the formation of remarkable pyramidal structures on the host cell envelope. Using whole-transcriptome sequencing, we present here a global map defining host and viral gene expression during the infection cycle of SIRV2 in its hyperthermophilic host S. islandicus LAL14/1. This information was used, in combination with a yeast two-hybrid analysis of SIRV2 protein interactions, to advance current understanding of viral gene functions. As a consequence of SIRV2 infection, transcription of more than one-third of S. islandicus genes was differentially regulated. While expression of genes involved in cell division decreased, those genes playing a role in antiviral defense were activated on a large scale. Expression of genes belonging to toxin-antitoxin and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems was specifically pronounced. The observed different degree of activation of various CRISPR-Cas systems highlights the specialized functions they perform. The information on individual gene expression and activation of antiviral defense systems is expected to aid future studies aimed at detailed understanding of the functions and interplay of these systems in vivo.
Voet, Marleen; Sismeiro, Odile; Dillies, Marie-Agnes; Jagla, Bernd; Coppee, Jean-Yves; Sezonov, Guennadi; Forterre, Patrick; van der Oost, John; Lavigne, Rob
Viral entry encompasses the initial steps of infection starting from virion host cell attachment to viral genome release. Given the dynamic interactions between the virus and the host, many questions related to viral entry can be directly addressed by live cell imaging. Recent advances in fluorescent labeling of viral and cellular components, fluorescence microscopy with high sensitivity and spatiotemporal resolution, and image analysis enabled studies of a broad spectrum across many viral entry steps, including virus-receptor interactions, internalization, intracellular transport, genomic release, nuclear transport, and cell-to-cell transmission. Collectively, these live cell imaging studies have not only enriched our understandings of the viral entry mechanisms, but also provided novel insights into basic cellular biology processes.
Sun, Eileen; He, Jiang; Zhuang, Xiaowei
Background: Integration of human papilloma virus (HPV) 16 DNA is considered an important genetic change in cervical lesion progression towards ICC. The viral E2 gene is often disrupted by this process, releasing suppression of viral E6\\/E7 oncogenes, a key factor for oncogenic progression. Objectives: To evaluate the physical status of HPV 16 E2 gene in cervical preneoplastic and neoplastic lesions
S. A Tonon; M. A Picconi; P. D Bos; J. B Zinovich; J Galuppo; L. V Alonio; A. R Teyssie
We studied the elastic properties and mechanical stability of viral capsids under external force-loading with computer simulations. Our approach allows the implementation of specific geometries corresponding to specific phages, such as ?29 and cowpea chlorotic mottle virus. We demonstrate how, in a combined numerical and experimental approach, the elastic parameters can be determined with high precision. The experimentally observed bimodality of elastic spring constants is shown to be of geometrical origin, namely the presence of pentavalent units in the viral shell. We define a criterion for capsid breakage that explains well the experimentally observed rupture. From our numerics we find a crossover from ?2/3 to ?1/2 for the dependence of the rupture force on the Föppl-von Kármán number, ?. For filled capsids, high internal pressures lead to a stronger destabilization for viruses with buckled ground states versus viruses with unbuckled ground states. Finally, we show how our numerically calculated energy maps can be used to extract information about the strength of protein–protein interactions from rupture experiments.
Buenemann, Mathias; Lenz, Peter
Bovine viral diarrhea virus was believed to be the cause of ill-thrift since birth, resulting in death of a Holstein calf. Bovine viral diarrhea virus was isolated from Peyer's patches and mesenteric lymph nodes, but serum neutralizing antibodies were not detected. The lymphoid depletion and myeloid suppression seen in this case may be a factor in the immune system dysfunction described for bovine viral diarrhea. Typical ulcerative lesions within the alimentary tract were not observed. PMID:3988595
Lloyd, K C; Morris, D D
OBJECTIVES:Viral hepatitis has previously been the major cause of acute liver failure (ALF) in the United States. We aimed to determine the incidence of viral hepatitis-related ALF and to compare the outcome and clinical and biochemical variables in patients with hepatitis A and B.METHODS:A total of 354 patients with ALF from multiple centers were screened for possible acute viral etiology.RESULTS:Forty-three
Frank Vinholt Schiødt; Timothy J. Davern; A. Obaid Shakil; Brendan McGuire; Grace Samuel; William M. Lee
Viral respiratory tract infections (RTI) pose a high burden on the youngest members of our society. Several risk factors are known for severe viral respiratory disease. However, a large proportion of the severe RTI cannot be explained by these risk factors. A growing body of evidence shows that the composition of the microbiota has a major influence on the training of both the mucosal and the systemic immune response and can thus potentially determine susceptibility for severe viral infections. In this review, we discuss the current evidence regarding the influence of bacterial colonization on the severity of viral respiratory infections. PMID:24220300
Vissers, M; de Groot, R; Ferwerda, G
Like their cellular host counterparts, many invading viral pathogens must contend with, modulate, and utilize the host cell’s chromatin machinery to promote efficient lytic infection or control persistent-latent states. While not intended to be comprehensive, this review represents a compilation of conceptual snapshots of the dynamic interplay of viruses with the chromatin environment. Contributions focus on chromatin dynamics during infection, viral circumvention of cellular chromatin repression, chromatin organization of large DNA viruses, tethering and persistence, viral interactions with cellular chromatin modulation machinery, and control of viral latency-reactivation cycles.
Knipe, David M.; Lieberman, Paul M.; Jung, Jae U.; McBride, Alison A.; Morris, Kevin V.; Ott, Melanie; Margolis, David; Nieto, Amelia; Nevels, Michael; Parks, Robin J.; Kristie, Thomas M.
Natural killer (NK) cells, as part of the innate immune system, play a key role in host defense against viral infections. Recent advances have indicated that NK cell activation and function are regulated by the interplay between inhibitory and activating signals. Thus, a better understanding of mechanisms responsible for NK cell activation and function in the control of viral infections will help develop NK cell-based therapies. In this review, we will first discuss how NK cells are activated in response to viral infections. We will then focus on the recruitment of activated NK cells to the site of infection as well as on NK cell effector mechanisms against virally infected cells.
Brandstadter, Joshua D.; Yang, Yiping
Abstract RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination of genetic change and natural selection. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of viral quasispecies and a method to infer its parameters from next-generation sequencing data. The model introduces position-specific probability tables over the sequence alphabet to explain the diversity that can be found in the population at each site. Recombination events are indicated by a change of state, allowing a single observed read to originate from multiple sequences. We present a specific implementation of the expectation maximization (EM) algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and applied to reads obtained from a clinical HIV sample.
Topfer, Armin; Zagordi, Osvaldo; Prabhakaran, Sandhya; Roth, Volker; Halperin, Eran
RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination of genetic change and natural selection. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of viral quasispecies and a method to infer its parameters from next-generation sequencing data. The model introduces position-specific probability tables over the sequence alphabet to explain the diversity that can be found in the population at each site. Recombination events are indicated by a change of state, allowing a single observed read to originate from multiple sequences. We present a specific implementation of the expectation maximization (EM) algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and applied to reads obtained from a clinical HIV sample. PMID:23383997
Töpfer, Armin; Zagordi, Osvaldo; Prabhakaran, Sandhya; Roth, Volker; Halperin, Eran; Beerenwinkel, Niko
Based on the theory of psychosomatic inhibition, we hypothesized that subjects who abstained from disclosing emotional material on a laboratory task would have poorer control of latent Epstein-Barr virus (as evidenced by high titers for the viral capsid antigen), and similarly, those subjects with psychometrically derived repressive interpersonal styles would show the highest Epstein-Barr viral capsid antigen titers (EBV-VCA). Eighty
BRIAN A. ESTERLING; MICHAEL H. ANTONI; MAHENDRA KUMAR; NEIL SCHNEIDERMAN
Viral hemorrhagic septicemia virus (VHSV) was first detected in the Laurentian Great Lakes in 2005 during a mortality event in the Bay of Quinte, Lake Ontario. Subsequent analysis of archived samples determined that the first known isolation of VHSV in the Laurentian Great Lakes was from a muskellunge Esox masquinongy collected in Lake St. Clair in 2003. By the end of 2008, mortality events and viral isolations had occurred in all of the Laurentian Great Lakes except Lake Superior. In 2009, a focused disease surveillance program was designed to determine whether VHSV was also present in Lake Superior. In this survey, 874 fish from 7 sites along the U.S. shoreline of Lake Superior were collected during June 2009. Collections were focused on nearshore species known to be susceptible to VHSV. All fish were dissected individually by using aseptic techniques and were tested for the presence of VHSV genetic material by use of a quantitative reverse transcription (qRT) polymerase chain reaction (PCR) targeting the viral nucleoprotein gene. Seventeen fish from two host species at two different sites tested positive at low levels for VHSV. All attempts to isolate virus in cell culture were unsuccessful. However, the presence of viral RNA was confirmed independently in five fish by using a nested PCR that targeted the glycoprotein (G) gene. Partial G gene sequences obtained from three fish were identical to the corresponding sequence from the original 2003 VHSV isolate (MI03) from muskellunge. These detections represent the earliest evidence for the presence of VHSV in Lake Superior and illustrate the utility of the highly sensitive qRT-PCR assay for disease surveillance in aquatic animals.
Cornwell, Emily R.; Eckerlin, Geofrey E.; Getchell, Rodman G.; Groocock, Geoffrey H.; Thompson, Tarin M.; Batts, William N.; Casey, Rufina N.; Kurath, Gael; Winton, James R.; Bowser, Paul R.; Bain, Mark B.; Casey, James W.
Background Whole genome sequencing of viruses and bacteriophages is often hindered because of the need for large quantities of genomic material. A method is described that combines single plaque sequencing with an optimization of Sequence Independent Single Primer Amplification (SISPA). This method can be used for de novo whole genome next-generation sequencing of any cultivable virus without the need for large-scale production of viral stocks or viral purification using centrifugal techniques. Methods A single viral plaque of a variant of the 2009 pandemic H1N1 human Influenza A virus was isolated and amplified using the optimized SISPA protocol. The sensitivity of the SISPA protocol presented here was tested with bacteriophage F_HA0480sp/Pa1651 DNA. The amplified products were sequenced with 454 and Illumina HiSeq platforms. Mapping and de novo assemblies were performed to analyze the quality of data produced from this optimized method. Results Analysis of the sequence data demonstrated that from a single viral plaque of Influenza A, a mapping assembly with 3590-fold average coverage representing 100% of the genome could be produced. The de novo assembled data produced contigs with 30-fold average sequence coverage, representing 96.5% of the genome. Using only 10 pg of starting DNA from bacteriophage F_HA0480sp/Pa1651 in the SISPA protocol resulted in sequencing data that gave a mapping assembly with 3488-fold average sequence coverage, representing 99.9% of the reference and a de novo assembly with 45-fold average sequence coverage, representing 98.1% of the genome. Conclusions The optimized SISPA protocol presented here produces amplified product that when sequenced will give high quality data that can be used for de novo assembly. The protocol requires only a single viral plaque or as little as 10 pg of DNA template, which will facilitate rapid identification of viruses during an outbreak and viruses that are difficult to propagate.
Rates of evolution span orders of magnitude among RNA viruses with important implications for viral transmission and emergence. Although the tempo of viral evolution is often ascribed to viral features such as mutation rates and transmission mode, these factors alone cannot explain variation among closely related viruses, where host biology might operate more strongly on viral evolution. Here, we analyzed sequence data from hundreds of rabies viruses collected from bats throughout the Americas to describe dramatic variation in the speed of rabies virus evolution when circulating in ecologically distinct reservoir species. Integration of ecological and genetic data through a comparative bayesian analysis revealed that viral evolutionary rates were labile following historical jumps between bat species and nearly four times faster in tropical and subtropical bats compared to temperate species. The association between geography and viral evolution could not be explained by host metabolism, phylogeny or variable selection pressures, and instead appeared to be a consequence of reduced seasonality in bat activity and virus transmission associated with climate. Our results demonstrate a key role for host ecology in shaping the tempo of evolution in multi-host viruses and highlight the power of comparative phylogenetic methods to identify the host and environmental features that influence transmission dynamics. PMID:22615575
Streicker, Daniel G; Lemey, Philippe; Velasco-Villa, Andres; Rupprecht, Charles E
Rates of evolution span orders of magnitude among RNA viruses with important implications for viral transmission and emergence. Although the tempo of viral evolution is often ascribed to viral features such as mutation rates and transmission mode, these factors alone cannot explain variation among closely related viruses, where host biology might operate more strongly on viral evolution. Here, we analyzed sequence data from hundreds of rabies viruses collected from bats throughout the Americas to describe dramatic variation in the speed of rabies virus evolution when circulating in ecologically distinct reservoir species. Integration of ecological and genetic data through a comparative Bayesian analysis revealed that viral evolutionary rates were labile following historical jumps between bat species and nearly four times faster in tropical and subtropical bats compared to temperate species. The association between geography and viral evolution could not be explained by host metabolism, phylogeny or variable selection pressures, and instead appeared to be a consequence of reduced seasonality in bat activity and virus transmission associated with climate. Our results demonstrate a key role for host ecology in shaping the tempo of evolution in multi-host viruses and highlight the power of comparative phylogenetic methods to identify the host and environmental features that influence transmission dynamics.
Streicker, Daniel G.; Lemey, Philippe; Velasco-Villa, Andres; Rupprecht, Charles E.
The innate immune response is initiated by the interaction of stereotypical pathogen components with genetically conserved receptors for extracytosolic pathogen-associated molecular patterns (PAMPs) or intracytosolic nucleic acids. In multicellular organisms, this interaction typically clusters signal transduction molecules and leads to their activations, thereby initiating signals that activate innate immune effector mechanisms to protect the host. In some cases programmed cell death—a fundamental form of innate immunity—is initiated in response to genotoxic or biochemical stress that is associated with viral infection. In this paper we will summarize innate immune mechanisms that are relevant to viral pathogenesis and outline the continuing evolution of viral mechanisms that suppress the innate immunity in mammalian hosts. These mechanisms of viral innate immune evasion provide significant insight into the pathways of the antiviral innate immune response of many organisms. Examples of relevant mammalian innate immune defenses host defenses include signaling to interferon and cytokine response pathways as well as signaling to the inflammasome. Understanding which viral innate immune evasion mechanisms are linked to pathogenesis may translate into therapies and vaccines that are truly effective in eliminating the morbidity and mortality associated with viral infections in individuals.
Kotwal, Girish J.; Hatch, Steven; Marshall, William L.
Perinatal infection with hepatitis C virus (HCV) is characterized by a wide range of alanine aminotransferase (ALT) levels. The mechanisms responsible for this variability are unknown. We examined whether the evolution of the HCV quasispecies was associated with different ALT profiles in perinatally infected children. Sequences within HCV envelope 1 and 2 genes, inclusive of the hypervariable region 1, the viral load, and the nascent humoral immunity were analyzed in serial serum samples from 12 perinatally infected children prospectively followed for a median of 53 months. These patients were selected to represent two different ALT patterns during the first year of life: 6 had high levels (maximum values ranging from 4.2 to 30 times the normal upper limit), and 6 had normal or slightly elevated levels (<2 times the normal upper limit). Two patterns of viral evolution were identified according to the ALT profiles. Biochemical evidence of hepatic injury was invariably associated with a mono- or oligoclonal viral population, whereas mild or no liver damage correlated with the early emergence of a heterogeneous viral quasispecies. Consistent with selective immune pressure, amino acid changes occurred almost exclusively within the hypervariable region 1 and were temporally associated with antibody seroconversion; at this time, the difference in genetic diversity between the two groups was highly significant (P = 0.002). The two patterns of viral evolution persisted over time and did not correlate with viral load or genotype. Our study demonstrates that, in perinatally infected children, the evolution of HCV quasispecies correlates with hepatic injury.
Farci, Patrizia; Quinti, Isabella; Farci, Stefania; Alter, Harvey J.; Strazzera, Rita; Palomba, Elvia; Coiana, Alessandra; Cao, Daniele; Casadei, Anna Maria; Ledda, Ritarella; Iorio, Raffaele; Vegnente, Angela; Diaz, Giacomo; Tovo, Pier-Angelo
Arenaviruses can cause severe hemorrhagic fever diseases in humans, with limited prophylactic or therapeutic measures. A small RING-domain viral protein Z has been shown to mediate the formation of virus-like particles and to inhibit viral RNA synthesis, although its biological roles in an infectious viral life cycle have not been directly addressed. By taking advantage of the available reverse genetics system for a model arenavirus, Pichinde virus (PICV), we provide the direct evidence for the essential biological roles of the Z protein's conserved residues, including the G2 myristylation site, the conserved C and H residues of RING domain, and the poorly characterized C-terminal L79 and P80 residues. Dicodon substitutions within the late (L) domain (PSAPPYEP) of the PICV Z protein, although producing viable mutant viruses, have significantly reduced virus growth, a finding suggestive of an important role for the intact L domain in viral replication. Further structure-function analyses of both PICV and Lassa fever virus Z proteins suggest that arenavirus Z proteins have similar molecular mechanisms in mediating their multiple functions, with some interesting variations, such as the role of the G2 residue in blocking viral RNA synthesis. In summary, our studies have characterized the biological roles of the Z protein in an infectious arenavirus system and have shed important light on the distinct functions of its domains in virus budding and viral RNA regulation, the knowledge of which may lead to the development of novel antiviral drugs. PMID:22761375
Wang, Jialong; Danzy, Shamika; Kumar, Naveen; Ly, Hinh; Liang, Yuying
The human immunodeficiency virus type 1 (HIV-1) promoter or long-terminal repeat (LTR) regulates viral gene expression by interacting with multiple viral and host factors. The viral transactivator protein Tat plays an important role in transcriptional activation of HIV-1 gene expression. Functional domains of Tat and its interaction with transactivation response element RNA and cellular transcription factors have been examined. Genetic variation within tat of different HIV-1 subtypes has been shown to affect the interaction of the viral transactivator with cellular and/or viral proteins, influencing the overall level of transcriptional activation as well as its action as a neurotoxic protein. Consequently, the genetic variability within tat may impact the molecular architecture of functional domains of the Tat protein that may impact HIV pathogenesis and disease. Tat as a therapeutic target for anti-HIV drugs has also been discussed.
Li, Luna; Dahiya, Satinder; Kortagere, Sandhya; Aiamkitsumrit, Benjamas; Cunningham, David; Pirrone, Vanessa; Nonnemacher, Michael R.; Wigdahl, Brian
All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the ‘Big Bang’ theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.
Villarreal, Luis P.
Communication technology is expanding at an incredibly rapid pace. Smart phones, tablet computers, and high speed wireless networks are all redefining the paradigm for communication. For marketers this means more avenues to reach potential customers. Viral marketing is one such avenue. Viral marketing is often defined as the modern incarnation of word of mouth marketing. This concept involves getting consumers
Viral marketing has attracted considerable concerns in recent years due to its novel idea of leveraging the social network to propagate the awareness of products. Specifically, viral marketing is to first target a limited number of users (seeds) in the social network by providing incentives, and these targeted users would then initiate the process of awareness spread by propagating the
Cheng Long; Raymond Chi-Wing Wong
This is a searchable database of the state science standards reflective of genetics content for each grade in the US. Genetics content includes standards on heredity, DNA, evolution, population ecology, some disease and biotechnology. One half of the standards are currently linked to websites that cover the material and more are vetted and linked every day. Activities to help teach the material will also be added soon.
Kenna Shaw (American Society of Human Genetics;)
Respiratory viral infections are frequent causes of morbidity in transplant patients. We screened symptomatic adult transplant recipients for respiratory viruses in a cohort of patients attending a referral medical center in Brazil. The duration of viral shedding and the prevalence of viral codetections were also determined. During a 1-year period (2011-2012), swabs were obtained from 50 patients. An in-house polymerase chain reaction panel designed to detect 10 viruses was used. Viruses were identified in 19 (38%) patients, particularly parainfluenza III (32%) and the respiratory syncytial virus (20%); multiple viruses were identified in 26% of patients. Prolonged viral shedding was observed with 60% of individuals excreting viruses for >10 days. The clinical and epidemiologic relevance of prolonged viral shedding remains to be determined. PMID:24289829
de Lima, C R A; Mirandolli, T B; Carneiro, L C; Tusset, C; Romer, C M; Andreolla, H F; Baethgen, L F; Pasqualotto, A C
Significant advances have been made in our understanding of the natural history and pathogenesis of viral encephalitides. The development of PCR has greatly increased our ability to diagnose viral infections of the central nervous system, particularly for herpes and enteroviral infections. Advancing knowledge has led to the recognition that some encephalitides can be reliably prevented by vaccination (eg, Japanese encephalitis and rabies). For other pathogens such as the arboviruses, the focus has been on prevention by vector control. Finally, effective therapy has been established for a very limited number of viral infections (eg, acyclovir for herpes simplex encephalitis). Other potentially useful treatments, such as pleconaril for enteroviral meningoencephalitis are under clinical evaluation. We review current understanding of viral encephalitides with particular reference to emerging viral infections and the availability of existing treatment regimens. PMID:11853816
Whitley, Richard J; Gnann, John W
Gene-based therapy is the intentional modulation of gene expression in specific cells to treat pathological conditions. This modulation is accomplished by introducing exogenous nucleic acids such as DNA, mRNA, small interfering RNA (siRNA), microRNA (miRNA) or antisense oligonucleotides. Given the large size and the negative charge of these macromolecules, their delivery is typically mediated by carriers or vectors. In this Review, we introduce the biological barriers to gene delivery in vivo and discuss recent advances in material sciences, nanotechnology and nucleic acid chemistry that have yielded promising non-viral delivery systems, some of which are currently undergoing testing in clinical trials. The diversity of these systems highlights the recent progress of gene-based therapy using non-viral approaches. PMID:25022906
Yin, Hao; Kanasty, Rosemary L; Eltoukhy, Ahmed A; Vegas, Arturo J; Dorkin, J Robert; Anderson, Daniel G
The measles virus (MV) nucleoprotein associates with the viral RNA genome to form the N-RNA complex, providing a template for viral RNA synthesis. In our previous study, major phosphorylation sites of the nucleoprotein were identified as S479 and S510. However, the functions of these phosphorylation sites have not been clarified. In this study, we rescued recombinant MVs (rMVs) whose phosphorylation sites in the nucleoprotein were substituted (rMV-S479A, rMV-S510A, and rMV-S479A/S510A) by reverse genetics and used them in subsequent analyses. In a one-step growth experiment, rMVs showed rapid growth kinetics compared with wild-type MV, although the peak titer of the wild-type MV was the same as or slightly higher than those of the rMVs. Time course analysis of nucleoprotein accumulation also revealed that viral gene expression of rMV was enhanced during the early phase of infection. These findings suggest that nucleoprotein phosphorylation has an important role in controlling viral growth rate through the regulation of viral gene expression. Conversely, multistep growth curves revealed that nucleoprotein-phosphorylation intensity inversely correlated with viral titer at the plateau phase. Additionally, the phosphorylation intensity of the wild-type nucleoprotein in infected cells was significantly reduced through nucleoprotein-phosphoprotein binding. Excessive nucleoprotein-phosphorylation resulted in lower stability against RNase and faster turnover of viral genomic RNA. These results suggest that nucleoprotein-phosphorylation is also involved in viral genomic RNA stability.
Sugai, Akihiro; Sato, Hiroki; Yoneda, Misako
The measles virus (MV) nucleoprotein associates with the viral RNA genome to form the N-RNA complex, providing a template for viral RNA synthesis. In our previous study, major phosphorylation sites of the nucleoprotein were identified as S479 and S510. However, the functions of these phosphorylation sites have not been clarified. In this study, we rescued recombinant MVs (rMVs) whose phosphorylation sites in the nucleoprotein were substituted (rMV-S479A, rMV-S510A, and rMV-S479A/S510A) by reverse genetics and used them in subsequent analyses. In a one-step growth experiment, rMVs showed rapid growth kinetics compared with wild-type MV, although the peak titer of the wild-type MV was the same as or slightly higher than those of the rMVs. Time course analysis of nucleoprotein accumulation also revealed that viral gene expression of rMV was enhanced during the early phase of infection. These findings suggest that nucleoprotein phosphorylation has an important role in controlling viral growth rate through the regulation of viral gene expression. Conversely, multistep growth curves revealed that nucleoprotein-phosphorylation intensity inversely correlated with viral titer at the plateau phase. Additionally, the phosphorylation intensity of the wild-type nucleoprotein in infected cells was significantly reduced through nucleoprotein-phosphoprotein binding. Excessive nucleoprotein-phosphorylation resulted in lower stability against RNase and faster turnover of viral genomic RNA. These results suggest that nucleoprotein-phosphorylation is also involved in viral genomic RNA stability. PMID:23966404
Sugai, Akihiro; Sato, Hiroki; Yoneda, Misako; Kai, Chieko
HIV/AIDS remains a chronic and incurable disease, in spite of the notable successes of highly active antiretroviral therapy. Gene therapy offers the prospect of creating genetic resistance to HIV that supplants the need for antiviral drugs. In sight of this goal, a variety of anti-HIV genes have reached clinical testing, including gene-editing enzymes, protein-based inhibitors, and RNA-based therapeutics. Combinations of therapeutic genes against viral and host targets are designed to improve the overall antiviral potency and reduce the likelihood of viral resistance. In cell-based therapies, therapeutic genes are expressed in gene modified T lymphocytes or in hematopoietic stem cells that generate an HIV-resistant immune system. Such strategies must promote the selective proliferation of the transplanted cells and the prolonged expression of therapeutic genes. This review focuses on the current advances and limitations in genetic therapies against HIV, including the status of several recent and ongoing clinical studies.
Burnett, John C.; Zaia, John A.; Rossi, John J.
Progeny virions of mammalian reoviruses are assembled in the cytoplasm of infected cells at discrete sites termed viral inclusions. Studies of temperature-sensitive (ts) mutant viruses indicate that nonstructural protein ?NS and core protein ?2 are required for synthesis of double-stranded (ds) RNA, a process that occurs at sites of viral assembly. We used confocal immunofluorescence microscopy and ts mutant reoviruses to define the roles of ?NS and ?2 in viral inclusion formation. In cells infected with wild-type (wt) reovirus, ?NS and ?2 colocalize to large, perinuclear structures that correspond to viral inclusions. In cells infected at a nonpermissive temperature with ?NS-mutant virus tsE320, ?NS is distributed diffusely in the cytoplasm and ?2 is contained in small, punctate foci that do not resemble viral inclusions. In cells infected at a nonpermissive temperature with ?2-mutant virus tsH11.2, ?2 is distributed diffusely in the cytoplasm and the nucleus. However, ?NS localizes to discrete structures in the cytoplasm that contain other viral proteins and are morphologically indistinguishable from viral inclusions seen in cells infected with wt reovirus. Examination of cells infected with wt reovirus over a time course demonstrates that ?NS precedes ?2 in localization to viral inclusions. These findings suggest that viral RNA-protein complexes containing ?NS nucleate sites of viral replication to which other viral proteins, including ?2, are recruited to commence dsRNA synthesis.
Becker, Michelle M.; Goral, Mehmet I.; Hazelton, Paul R.; Baer, Geoffrey S.; Rodgers, Steven E.; Brown, Earl G.; Coombs, Kevin M.; Dermody, Terence S.
The viral diseases of carp and catfish for which vaccines have been produced are spring viraemia of carp (SVC), grass carp haemorrhage disease (GCHD) and channel catfish virus disease (CCVD). Field trials of a commercially produced injectable vaccine conducted over several years have shown that carp can be protected against SVC. However the supporting data were predominantly qualitative rather than quantitative. Large-scale field trials of an experimental oral attenuated vaccine against SVC virus over a five year period were successful, and no reversion to virulence of the vaccine was recorded. Injectable inactivated and attenuated vaccines against GCHD have predominantly been tested under laboratory conditions, although a small number of field trials have been reported. In such trials of bath and injectable vaccines, survival rates of 50-90% were achieved. In China, commercially available vaccines are being used against GCHD. Only laboratory trials of vaccines against CCVD have been reported. Bath vaccination of eggs of fry with a subunit vaccine and bath immunisation of fingerlings with an attenuated virus vaccine have been successful. Problems with current approaches and areas for research are discussed. PMID:9270851
This book on the subject of medical genetics is a textbook aimed at a very broad audience: principally, medical students, nursing students, graduate, and undergraduate students. The book is actually a primer of general genetics as applied to humans and provides a well-balanced introduction to the scientific and clinical basis of human genetics. The twelve chapters include: Introduction, Basic Cell Biology, Genetic Variation, Autosomal Dominant and Recessive Inheritance, Sex-linked and Mitochondrial Inheritance, Clinical Cytogenetics, Gene Mapping, Immunogenetics, Cancer Genetics, Multifactorial Inheritance and Common Disease, Genetic Screening, Genetic Diagnosis and Gene Therapy, and Clinical Genetics and Genetic Counseling.
Jorde, L.B.; Carey, J.C.; White, R.L.
Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.
Wang, Lui; Bayer, Steven E.
The facile two-dimensional fabrication of micron-scale patterns of ordered-nanoscale structures on flexible substrates has numerous broad implications, including sacrificial templates for further assembly, deposition or material removal. Previous examinations of block-copolymer assembly on micron-scale patterns with topological and/or chemical relief have demonstrated the ability to not only dictate the larger superstructure of the surface but also to impact the local nano-scale self-assembly and defect stability via confinement. These processes are examined with respect to the surface directed assembly of colloidal particles, specifically rod-like Tobacco Mosaic Virus (TMV) and iscohoderhal viruses Wiseana Iridovirus (WIV) and MS2. The unique surface chemistry and shapes provide a complement to traditional colloidal building-blocks. Initially, high throughput processing by convective self assembly (CSA) with orthogonal temperature gradients is combined with chemical modification of Silicon surfaces via soft-lithography to determine the key processing parameters for monolayer assembly. The impact of the viral shape (rod v. iscohodra) as well as the critical range of enthalpic interactions between the virus and substrate that control in-plane order and pattern formation will be discussed.
Wargacki, S.; Naik, R.; Phillips, D.; Francis, M.; Ward, V.; Thomas, E.; Vaia, R. A.
Enzootic bronchopneumonia (EBP) is an infectious, multifactorial respiratory disease of cattle. Different viruses may be involved in its pathogenesis. In this study an adapted method of endoscopic bronchoalveolar lavage (BAL) of caudal parts of the right cranial lung lobe was established and evaluated. The obtained bronchoalveolar lavage fluid (BALF) served as template for the detection of BRSV, BPIV-3 and BCoV specific nucleic acids by RT-PCR. BALF samples of 44 cattle affected with respiratory disease were compared to nasal swabs in their reliability to detect the causative agent(s). In 6/7 animals tested positive for BRSV, RNA of this virus was detected in the BALF, in 4 animals it could be found in the nasal swabs. In two of the three BPIV-3 positive animals, the BALF was the only material that tested positive. The most reliable samples for detection of 15 BCoV positive animals were the nasal swabs. BAL was easy to perform, it led to severe coughing in one case and moderate worsening of dyspnoe in three cases. In conclusion this study shows that BAL of the right cranial lung lobe is in many cases the only tool to detect BRSV and BPIV-3, major viral triggers of EBP. PMID:21971671
Iglseder, A; Franz, S; Benetka, V; Möstl, K; Latif, M; Walk, K; Baumgartner, W
Viruses that maintain their genomes as extrachromosomal circular DNA molecules and establish infection in actively dividing cells must ensure retention of their genomes within the nuclear envelope in order to prevent genome loss. The loss of nuclear membrane integrity during mitosis dictates that paired host cell chromosomes are captured and organized by the mitotic spindle apparatus before segregation to daughter cells. This prevents inaccurate chromosomal segregation and loss of genetic material. A similar mechanism may also exist for the nuclear retention of extrachromosomal viral genomes or episomes during mitosis, particularly for genomes maintained at a low copy number in latent infections. It has been heavily debated whether such a mechanism exists and to what extent this mechanism is conserved among diverse viruses. Research over the last two decades has provided a wealth of information regarding the mechanisms by which specific tumour viruses evade mitotic and DNA damage checkpoints. Here, we discuss the similarities and differences in how specific viruses tether episomal genomes to host cell chromosomes during mitosis to ensure long-term persistence.
Feeney, Katherine M.; Parish, Joanna L.
We have developed nanoparticles based on Murine Leukemia Virus virus-like-particles (VLPs) that efficiently deliver therapeutic bioactive proteins in their native state into target cells. Nuclear transcription factors and toxic proteins were incorporated into the VLPs from stable producer cells without transducing viral-encoded genetic material. Delivery of nuclear transcription factors required incorporation of nuclear export signals (NESs) into the vector backbone for the efficient formation of VLPs. In the presence of an appropriate targeting Env glycoprotein, transcription factors delivered and activated nuclear transcription in the target cells. Additionally, we show delivery of the bacterial toxin, MazF, which is an ACA-specific mRNA interferase resulted in the induction of cell death. The stable producer cells are protected from the toxin through co-expression of the anti-toxin MazE and continuously released MazF incorporating VLPs. This highly adaptable platform can be harnessed to alter and regulate cellular processes by bioactive protein delivery. PMID:24997480
Wu, Dai-Tze; Roth, Monica J
Viruses are the most common biological entities in the oceans by an order of magnitude. Diversity of these viruses undoubtedly plays an important role in controlling bacterial populations and biogeochemical cycles in the marine environment. However, very little is known about the diversity of marine viral communities. Here we report the first genomic analysis of uncultured viral communities from two nearshore marine water samples and one marine sediment sample. In all three marine libraries, over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is novel. The most common significant hits amongst the known sequences were to viruses. The viral hits included sequences from all the major families of dsDNA tailed phage, as well as some algal viruses. BLAST analysis of the sequence data suggested fundamental differences between the viral communities. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in the water communities, which were estimated to contain between 374 and 7114 viral types. Diversity of the sediment community was significantly higher. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.
Breitbart, M.; Salamon, P.; Andresen, B.; Mahaffy, J. M.; Segall, A. M.; Mead, D.; Azam, F.; Rohwer, F.
Among the different subsets of dendritic cells (DC), plasmacytoid dendritic cells (PDC) play a unique role in secreting large amounts of type I interferons upon viral stimulation, but their efficiency as antigen-presenting cells has not been completely characterized. We show here, by flow cytometry, with human primary blood PDC and with a PDC cell line, that PDC display poor endocytic capacity for soluble or cellular antigens when compared to monocyte-derived myeloid DC. However, immature PDC efficiently take up cellular material from live influenza-exposed cells, subsequently mature and cross-present viral antigens very efficiently to specific CD8+ T cells. Therefore, during viral infection PDC not only secrete immunomodulatory cytokines, but also recognize infected cells and function as antigen cross-presenting cells to trigger the anti-viral immune response.
Lui, Gabrielle; Manches, Olivier; Angel, Juliette; Molens, Jean-Paul
Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we suggest that a strong program concept of genetic material can be used as a successful heuristic in certain areas of synthetic biology. Its application requires control of causal context, and may stand in need of a modular decomposition of the target system. We relate different modularity concepts to the discussion of genetic causation and point to possible advantages of and important limitations to seeking modularity in synthetic biology systems. PMID:23591049
Oftedal, Gry; Parkkinen, Veli-Pekka
Adeno-associated virus (AAV) is an important vector system for human gene therapy. Although use of AAV serotypes can result in efficient myocardial gene transfer, improvements in the transduction efficiency and specificity are still required. As a method for artificial modification and selection of gene function, directed evolution has been used for diverse applications in genetic engineering of enzymes and proteins. Since 2000, pioneering work has been performed on directed evolution of viral vectors. We further attempted to evolve the AAV using DNA shuffling and in vivo biopanning in a mouse model. An AAVM41 mutant was characterized, which was found to have improved transduction efficiency and specificity in myocardium, an attribute unknown for any natural AAV serotypes. This review focuses on the development of AAV vector for cardiac gene transfer, the history of directed evolution of viral vectors, and our creation of a cardiotropic AAV, which might have implications for the future design and application of viral vectors.
A molecular genetic analysis has been combined with an in vitro biochemical approach to define the functional interactions required for nucleotidyl protein formation during poliovirus RNA synthesis. A site-directed lesion into the hydrophobic domain of a viral membrane protein produced a mutant virus that is defective in RNA synthesis at 39 degrees C. The phenotypic expression of this lesion affects initiation of RNA synthesis, in vitro uridylylation of the genome-linked protein (VPg), and the in vivo synthesis of plus-strand viral RNAs. Our results support a model that employs a viral membrane protein as carrier for VPg in the initiation of plus-strand RNA synthesis. Our data also suggest that a separate mechanism could be used in the initiation of minus-strand RNA synthesis, thereby providing a means for strand-specific regulation of picornavirus RNA replication. Images
Giachetti, C; Semler, B L
Genetic algorithms (GAs) are search methods based on principles of natural selection and genetics (Fraser, 1957;Bremermann, 1958;Holland, 1975). We start with a brief introduction to simple genetic algorithms and associated terminology.
Kumara Sastry; David Goldberg; Graham Kendall
This study considers multi-objective optimal design of the fiber reinforced symmetric-balanced laminated composites using genetic algorithms. MATLAB Genetic Algorithm and Direct Search Toolbox is used to obtain Pareto-optimal design for three different model problems. The objectives of the problems are to maximize the Young's moduli and minimize the coefficient of thermal expansion (CTE) simultaneously for 8 and 16 layered carbon\\/epoxy
Levent Aydin; H. Secil Artem
The genetic variability of classical swine fever virus was studied by comparative nucleotide sequence analysis of 76 virus isolates, collected during a half century from three continents. Parts of the E2 (gp55) and the polymerase gene coding regions of the viral genome were amplified by RT-PCR and DNA fragments of 254 and 207 bp, respectively, were sequenced. The comparative sequence
Š Vil?ek; T Stadejek; A Ballagi-Pordány; J. P Lowings; D. J Paton; S Belák
The assessment of potential environmental impacts of genetically improved viral pesticides will include an evaluation of the properties of the foreign gene product(s) as well as the biological properties of altered virus itself. It is anticipated that in the near future several t...
In recent years, therapeutic use of engineered particles on the 1-1,000 nm scale has gained popularity; these nanoparticles have been developed for use in drug delivery, gene therapy, vaccine preparation, and diagnostics. Often, viral proteins are utilized in the design of such species, and outlined here are completed studies on the in vitro assembly of nanoparticles derived from two very different viral systems. The incorporation of the human immunodeficiency virus (HIV) envelope glycoprotein precursor gp160 into phospholipid bilayer nanodiscs is discussed as a potential platform for vaccine design; efforts were successful, however yield currently limits the practical application of this approach. The utility of bacteriophage lambda procapsids and virus-like particles in therapeutic nanoparticle design is also outlined, as are efforts toward the structural and thermodynamic characterization of a urea-triggered capsid maturation event. It is demonstrated that lambda virus-like particles can be assembled from purified capsid and scaffolding proteins, and that these particles undergo urea-triggered maturation and in vitro decoration protein addition similar to that seen in lambda procapsids. The studies on lambda provided materials for the further development of nanoparticles potentially useful in a clinical setting, as well as shedding light on critical viral assembly and maturation events as they may take place in vivo.
Gene and drug therapy for organ-specific diseases in part depends on the efficient delivery to a particular region of the body. We examined the biodistribution of a viral envelope commonly used as a nanoscale gene delivery vehicle using positron emission tomography (PET) and investigated the magnetic alteration of its biodistribution. Iron oxide nanoparticles and 18 F-fluoride were encapsulated by hemagglutinating virus of Japan envelopes (HVJ-Es). HVJ-Es were then injected intravenously in the rat and imaged dynamically using high-resolution PET. Control subjects received injections of encapsulated materials alone. For magnetic targeting, permanent magnets were fixed on the head during the scan. Based on the quantitative analysis of PET images, HVJ-Es accumulated in the liver and spleen and activity remained higher than control subjects for 2 h. Histological sections of the liver confirmed imaging findings. Pixel-wise activity patterns on coregistered PET images of the head showed a significantly different pattern for the subjects receiving magnetic targeting as compared to all control groups. Imaging demonstrated the initial biodistribution of a viral envelope within the rodent by providing quantitative behavior over time and in specific anatomical regions. Magnetic force altered the biodistribution of the viral envelope to a target structure, and could enable region-specific delivery of therapeutic vehicles noninvasively.
Flexman, Jennifer A.; Cross, Donna J.; Lewellen, Barbara L.; Miyoshi, Sosuke; Kim, Yongmin
Infectious gastroenteritis is a common cause of hospitalization in the pediatric population. The most frequent cause of gastroenteritis is viral in origin. The purpose of this study was to compare a rapid modified negative-staining TEM method with the conventional pseudoreplica technique in detection of viral particles in fecal samples from children with viral gastroenteritis. The modified negative-staining method resulted in a significantly higher (2.5 ± 0.5, p = 0.02) viral rating score than that for the conventional pseudoreplica technique (1.7 ± 0.4). In addition, the preparation time for the negative-staining method was approximately one fifth that for the conventional pseudoreplica technique. Rapid diagnosis of viral gastroenteritis may be made by ultrastructural detection of viral particles in fecal samples using the negative staining technique.
Hicks, M. John; Barrish, James P.; Hayes, Elizabeth S.; Leer, Laurie C.; Estes, Mary K.; Cubitt, W. D.
The monograph on the pathomorphology of viral and hyperergic encephalitides and bears the mark of original research achievements. The clinico-pathological correlations given in most of the chapters and references to the animal pathology are particularly v...
The application of electron microscopic techniques in the study of human gastroenteritis led in the 1970's to the identification of new viral agents that had previously escaped detection by routine cell culture procedures. These agents have been the focus...
F. P. Williams
Viral miRNAs, ?22nt RNA molecules which post-transcriptionally regulate gene expression, are emerging as important tools in immune evasion. Viral infection is a complex process that requires immune evasion in order to establish persistent life-long infection of the host. During this process viruses express both protein-coding and non-coding genes, which help to modulate the cellular environment making it more favorable for infection. In the last decade, it was uncovered that DNA viruses express a diverse and abundant pool of small non-coding RNA molecules, called microRNAs (miRNAs). These virally encoded miRNAs are non-immunogenic and therefore are important tools used to evade both innate and adaptive immune responses. This review aims to summarize our current knowledge of herpesvirus- and polyomavirus-encoded miRNAs, and how they contribute to immune evasion by targeting viral and/or host cellular genes.
Boss, Isaac W.; Renne, Rolf
Viral fitness is an active area of research, with recent work involving an expanded number of human, non-human vertebrate, invertebrate, plant, and bacterial viruses. Many publications deal with RNA viruses associated with major disease emergence events, such as HIV-1, influenza virus, and Dengue virus. Study topics include drug resistance, immune escape, viral emergence, host jumps, mutation effects, quasispecies diversity, and mathematical models of viral fitness. Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. This is essential for a more integrated understanding of overall viral fitness, with implications for disease management in the future.
Wargo, Andrew R.; Kurath, Gael
The combination of nebulized epinephrine and high dose dexamethasone, or nebulized hypertonic saline, are promising new therapeutic strategies for viral bronchiolitis in the young infant. However, further research is needed before a general recommendation can be given. PMID:23409652
Rochat, I; Hafen, G
The project objectives are: To evaluate the enterovirus concentration of oysters sampled from a prohibited reef versus the 'natural viral background' of a reef bacteriologically approved for public shellfish collection. Samples for enterovirus detection w...
R. D. Ellender D. W. Cook
Interim report on the genetic and animal toxicity testing of SRC-I products, intermediates, and waste materials. Appendix C. Chemical evaluation of SRC samples for genetic toxicity testing - basic program reports
This Appendix presents the reports submitted by SRI regarding the chemical analyses of 32 samples done in support of the genetic toxicity testing. This chemical characterization provided an analytical signature for comparison, to demonstrate that there had been no gross changes in the nature of the chemicals stored by SRI during their investigations. Both ICRC and SRI considered it important
B. Z. Drozdowicz; C. M. Kelly
Many recent and significant advances in the field of chronic viral hepatitis, including therapy, suggest that an update on chronic hepatitis is timely.?Chronic hepatitis B virus infection remains a significant worldwide cause of liver cirrhosis and hepatocellular carcinoma, despite the wide availability of a long established and effective vaccine. Transmission occurs via perinatal, sexual, and parenteral routes (particularly intravenous drug abuse and although blood products still carry a risk, this is now extremely low in Western countries). Only a minority of infected adult cases develop chronic hepatitis but in children under 1 year, 90% develop chronic hepatitis. The clinical spectrum of chronic liver injury ranges from mild inflammation to end stage liver cirrhosis. Interferon alfa has been the mainstay of treatment for patients with active disease but nucleoside analogues (lamivudine and adefovir) are now available with similar efficacy. Patients with end stage liver disease and hepatocellular carcinoma can be offered transplantation but infection in the graft is commonplace. The combination of hepatitis B immunoglobulin and newer antiviral drugs reduce the incidence and severity of graft infection significantly.?The hepatitis C virus epidemic of the latter half of the 20th century now affects more than 1% of populations worldwide. This RNA virus is spread parenterally and is becoming the leading indication for liver transplantation. The majority of patients develop chronic hepatitis, which may be progressive, evolving to significant liver disease (cirrhosis or hepatocellular carcinoma) in about 20% cases after decades. Treatment with the combination of interferon alfa and ribavirin is successful in up to 40% cases. Liver transplantation is a therapeutic option for some but graft infection is universal and often complicated by progressive liver fibrosis. A vaccine remains a remote prospect so that prevention is crucial.?Hepatitis D virus infection occurs on a background of hepatitis B virus infection and can also cause liver damage. The response to antiviral therapy is poor.?The newer "hepatitis" viruses G and TT do not cause significant liver injury.???Keywords: hepatitis
Walsh, K; Alexander, G
Well-studied innate immune systems exist throughout bacteria and archaea, but a more recently discovered genomic locus may offer prokaryotes surprising immunological adaptability. Mediated by a cassette-like genomic locus termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), the microbial adaptive immune system differs from its eukaryotic immune analogues by incorporating new immunities unidirectionally. CRISPR thus stores genomically recoverable timelines of virus-host coevolution in natural organisms refractory to laboratory cultivation. Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. This 'trailer-end conservation' occurs despite rapid viral mutation and despite rapid prokaryotic genomic deletion. The trailer-ends of many reconstructed CRISPR loci are also largely identical across a population. 'Trailer-end clonality' occurs despite predictions of host immunological diversity due to negative frequency dependent selection (kill the winner dynamics). Statistical clustering and model simulations explain this lack of diversity by capturing rapid selective sweeps by highly immune CRISPR lineages. Potentially explaining 'trailer-end conservation,' we record the first example of a viral bloom overwhelming a CRISPR system. The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. Our results thus link documented patterns of genomic conservation in CRISPR loci to an evolutionary advantage against persistent viruses. By maintaining old immunities, selection may be tuning CRISPR-mediated immunity against viruses reemerging from lysogeny or migration. PMID:22532794
Weinberger, Ariel D; Sun, Christine L; Pluci?ski, Mateusz M; Denef, Vincent J; Thomas, Brian C; Horvath, Philippe; Barrangou, Rodolphe; Gilmore, Michael S; Getz, Wayne M; Banfield, Jillian F
Viral miRNAs, ~22nt RNA molecules which post-transcriptionally regulate gene expression, are emerging as important tools in immune evasion. Viral infection is a complex process that requires immune evasion in order to establish persistent life-long infection of the host. During this process viruses express both protein-coding and non-coding genes, which help to modulate the cellular environment making it more favorable for
Isaac W. Boss; Rolf Renne
New viral infections of the nervous system have been appearing with great regularity. Some result from the evolution of new\\u000a agents and others from the entry of viruses into new hosts or environments. The emergence of neurovirulent enteroviruses causing\\u000a a paralytic poliomyelitis syndrome and rhomboencephalitis represent the evolution of new human viruses. Most emerging viral\\u000a infections represent movement of an
Richard T. Johnson
Coinfection with HIV and viral hepatitis substantially alters the natural course of viral hepatitis as well as its management.\\u000a Therapy for infection with hepatitis B virus (HBV) in HIV-coinfected patients requires consideration of several factors, such\\u000a as whether the antiviral activity of a particular agent is specific for HBV or for both viruses, the potential for drug resistance\\u000a and cross-resistance,
Hussien Elsiesy; Douglas Dieterich
The flow of genetic information from sites of transcription within the nucleus to the cytoplasmic translational machinery of eukaryotic cells is obstructed by a physical blockade, the nuclear double membrane, which must be overcome in order to adhere to the central dogma of molecular biology, DNA makes RNA makes protein. Advancement in the field of cellular and molecular biology has painted a detailed picture of the molecular mechanisms from transcription of genes to mRNAs and their processing that is closely coupled to export from the nucleus. The rules that govern delivering messenger transcripts from the nucleus must be obeyed by influenza A virus, a member of the Orthomyxoviridae that has adopted a nuclear replication cycle. The negative-sense genome of influenza A virus is segmented into eight individual viral ribonucleoprotein (vRNP) complexes containing the viral RNA-dependent RNA polymerase and single-stranded RNA encapsidated in viral nucleoprotein. Influenza A virus mRNAs fall into three major categories, intronless, intron-containing unspliced and spliced. During evolutionary history, influenza A virus has conceived a way of negotiating the passage of viral transcripts from the nucleus to cytoplasmic sites of protein synthesis. The major mRNA nuclear export NXF1 pathway is increasingly implicated in viral mRNA export and this review considers and discusses the current understanding of how influenza A virus exploits the host mRNA export pathway for replication. PMID:23807439
York, Ashley; Fodor, Ervin
The use of viral vectors is a method for introducing foreign genes into various animal species. Vectors based on retro-, adeno-, flavi-, and parvoviruses have been used for research in animal species of agricultural importance, such as chickens, quail, swine, cows, goats, sheep, fish, crustaceans, and mollusks. Viral vectors allow for efficient transgenic integration into host genome or for transient expression of the transgenic construct in somatic tissues. Because of that, viral vectors are important tools for research and potentially other biotechnology applications such as improving animal production qualities and introducing disease resistance, thus improving food quality and safety. Other uses may include generating animal models of human diseases and using animals as bioreactors for production of therapeutic proteins. Each vector type provides a unique set of advantages and limitations, which are in some cases specific to an animal species or a method of introduction. This article discusses viral vector characteristics and potential applications in agriculturally important animal species. It discusses advantages and disadvantages of using viral vectors in genetic engineering of agricultural animals. PMID:19937496
Modric, Tomislav; Mergia, Ayalew
An important goal of contemporary HIV type 1 (HIV-1) research is to identify cellular cofactors required for viral replication. The HIV-1 Rev protein facilitates the cytoplasmic accumulation of the intron-containing viral gag-pol and env mRNAs and is required for viral replication. We have previously shown that a cellular protein, human Rev-interacting protein (hRIP), is an essential Rev cofactor that promotes the release of incompletely spliced HIV-1 RNAs from the perinuclear region. Here, we use complementary genetic approaches to ablate hRIP activity and analyze HIV-1 replication and viral RNA localization. We find that ablation of hRIP activity by a dominant-negative mutant or RNA interference inhibits virus production by mislocalizing Rev-directed RNAs to the nuclear periphery. We further show that depletion of endogenous hRIP by RNA interference results in the loss of viral replication in human cell lines and primary macrophages; virus production was restored to wild-type levels after reintroduction of hRIP protein. Taken together, our results indicate that hRIP is an essential cellular cofactor for Rev function and HIV-1 replication. Because hRIP is not required for cell viability, it may be an attractive target for the development of new antiviral strategies. PMID:15749819
Yu, Zhong; Sánchez-Velar, Nuria; Catrina, Irina E; Kittler, Ellen L W; Udofia, Enyeneama B; Zapp, Maria L
Metagenomics and a panmicrobial microarray were used to examine eight live-attenuated viral vaccines. Viral nucleic acids in trivalent oral poliovirus (OPV), rubella, measles, yellow fever, varicella-zoster, multivalent measles/mumps/rubella, and two rotavirus live vaccines were partially purified, randomly amplified, and pyrosequenced. Over half a million sequence reads were generated covering from 20 to 99% of the attenuated viral genomes at depths reaching up to 8,000 reads per nucleotides. Mutations and minority variants, relative to vaccine strains, not known to affect attenuation were detected in OPV, mumps virus, and varicella-zoster virus. The anticipated detection of endogenous retroviral sequences from the producer avian and primate cells was confirmed. Avian leukosis virus (ALV), previously shown to be noninfectious for humans, was present as RNA in viral particles, while simian retrovirus (SRV) was present as genetically defective DNA. Rotarix, an orally administered rotavirus vaccine, contained porcine circovirus-1 (PCV1), a highly prevalent nonpathogenic pig virus, which has not been shown to be infectious in humans. Hybridization of vaccine nucleic acids to a panmicrobial microarray confirmed the presence of endogenous retroviral and PCV1 nucleic acids. Deep sequencing and microarrays can therefore detect attenuated virus sequence changes, minority variants, and adventitious viruses and help maintain the current safety record of live-attenuated viral vaccines.
Victoria, Joseph G.; Wang, Chunlin; Jones, Morris S.; Jaing, Crystal; McLoughlin, Kevin; Gardner, Shea; Delwart, Eric L.
Selection of antigens for therapeutic vaccination against chronic viral infections is complicated by pathogen genetic variations. We tested whether antigens present during persistent viral infections could provide a personalized antigenic reservoir for therapeutic T cell expansion in humans. We focused our study on the HBV surface antigen (HBsAg), which is present in microgram quantities in the serum of chronic HBV patients. We demonstrated by quantitative fluorescent microscopy that, out of 6 professional APC populations in the circulation, only CD14 monocytes (MNs) retained an HBsAg depot. Using TCR-redirected CD8+ T cells specific for MHC-I–restricted HBV epitopes, we showed that, despite being constantly exposed to antigen, ex vivo–isolated APCs did not constitutively activate HBV-specific CD8+ T cells. However, differentiation of HBsAg+ CD14 MNs from chronic patients to MN-derived DCs (moDCs) induced cross-presentation of the intracellular reservoir of viral antigen. We exploited this mechanism to cross-present circulating viral antigen and showed that moDCs from chronically infected patients stimulated expansion of autologous HBV-specific T cells. Thus, these data demonstrate that circulating viral antigen produced during chronic infection can serve as a personalized antigenic reservoir to activate virus-specific T cells.
Gehring, Adam J.; Haniffa, Muzlifah; Kennedy, Patrick T.; Ho, Zi Zong; Boni, Carolina; Shin, Amanda; Banu, Nasirah; Chia, Adeline; Lim, Seng Gee; Ferrari, Carlo; Ginhoux, Florent; Bertoletti, Antonio
Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis.
Wood-Charlson, Elisha M.; Suttle, Curtis A.; van Oppen, Madeleine J. H.
From almost negligible amounts in 1970, the quantity of cultivated shrimp (~3 million metric tons in 2007) has risen to approach that of the capture fishery and it constitutes a vital source of export income for many countries. Despite this success, viral diseases along the way have caused billions of dollars of losses for shrimp farmers. Desire to reduce the losses to white spot syndrome virus in particular, has stimulated much research since 2000 on the shrimp response to viral pathogens at the molecular level. The objective of the work is to develop novel, practical methods for improved disease control. This review covers the background and limitations of the current work, baseline studies and studies on humoral responses, on binding between shrimp and viral structural proteins and on intracellular responses. It also includes discussion of several important phenomena (i.e., the quasi immune response, viral co-infections, viral sequences in the shrimp genome and persistent viral infections) for which little or no molecular information is currently available, but is much needed. PMID:20393775
Flegel, T W; Sritunyalucksana, Kallaya
Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis. PMID:24847321
Weynberg, Karen D; Wood-Charlson, Elisha M; Suttle, Curtis A; van Oppen, Madeleine J H
The purpose of this report is to design and develop a tool for analysis of raw sequence read data from viral metagenomics experiments. The tool should compare read sequences of known viral nucleic acid sequence data and enable a user to attempt to determine, with some degree of confidence, what virus groups may be present in the sample. This project was conducted in two phases. In phase 1 we surveyed the literature and examined existing metagenomics tools to educate ourselves and to more precisely define the problem of analyzing raw read data from viral metagenomic experiments. In phase 2 we devised an approach and built a prototype code and database. This code takes viral metagenomic read data in fasta format as input and accesses all complete viral genomes from Kpath for sequence comparison. The system executes at the UNIX command line, producing output that is stored in an Oracle relational database. We provide here a description of the approach we came up with for handling un-assembled, short read data sets from viral metagenomics experiments. We include a discussion of the current MetaView code capabilities and additional functionality that we believe should be added, should additional funding be acquired to continue the work.
Zhou, C; Smith, J
The treatment of axonal disorders, such as diseases associated with axonal injury and degeneration, is limited by the inability to directly target therapeutic protein expression to injured axons. Current gene therapy approaches rely on infection and transcription of viral genes in the cell body. Here we describe an approach to target gene expression selectively to axons. Using a genetically engineered mouse containing epitope-labeled ribosomes, we find that neurons in adult animals contain ribosomes in distal axons. To use axonal ribosomes to alter local protein expression, we utilized a Sindbis virus containing an RNA genome that has been modified so that it can be directly used as a template for translation. Selective application of this virus to axons leads to local translation of heterologous proteins. Furthermore, we demonstrate that selective axonal protein expression can be used to modify axonal signaling in cultured neurons, enabling axons to grow over inhibitory substrates typically encountered following axonal injury. We also show that this viral approach also can be used to achieve heterologous expression in axons of living animals, indicating that this approach can be used to alter the axonal proteome in vivo. Together, these data identify a novel strategy to manipulate protein expression in axons, and provides a novel approach for using gene therapies for disorders of axonal function.
Walker, Breset A.; Hengst, Ulrich; Kim, Hyung Joon; Jeon, Noo Li; Schmidt, Eric F.; Heintz, Nathaniel; Milner, Teresa A.; Jaffrey, Samie R.
Comprehensive presentation of Mendelian genetics enhanced with schematic diagrams and color photos. A sidebar of topics includes Variations to Mendel's First Law, Pedigree Analysis, Mendel's Second Law, Pleiotropy, Epistasis, Modifier Genes, Penetrance and Expressivity, Study Questions, Mendelian Genetics Overheads, Mendelian Genetics WWW Links Genetic Topics
This book contains 70 selections. Some of the selection titles are: Structure of the Gene Encoding of Immunodominant Surface Antigen on the Sprozoite of the Human Malaria Parasite Plasmodium falciparum; Cloning and Expression in Bacteria of the Genes for Merozite-specific Antigens from the Malaria Parasite Plasmodium falciparum; A Major Surface Antigen of Plasmodium falciparum in Merozoites: Studies on the Protein and its Gene; Genetic Construction of Cholera Vaccine Prototypes; and Viral Genes, Cytotoxic T Lymphocytes and Immunity.
Lerner, R.A.; Chanock, R.M.; Brown, F.
Two-photon scanning microscopy has advanced our understanding of neural signaling in non-mammalian species and mammals. Various developments are needed to perform two-photon scanning microscopy over prolonged periods in non-human primates performing a behavioral task. In striate cortex in two macaque monkeys, cortical neurons were transfected with a genetically encoded fluorescent calcium sensor, memTNXL, using AAV1 as a viral vector. By
Barbara Heider; Jason L. Nathanson; Ehud Y. Isacoff; Edward M. Callaway; Ralph M. Siegel; Pedro R. Lowenstein
Two pea seedborne mosaic potyvirus (PSbMV) isolates, P-1 DPD1 (P-l), which is highly seed- transmitted, and P-4 NY (P-4), which is rarely seed- transmitted, and chimeras between P-1 and P-4 were analysed to map the viral genetic determinants of seed transmission. Infectivity of chimeric viruses was evaluated by inoculating Pisum sativum with RNA transcribed in vitro from recombinant full- length
I. E. Johansen; W. G. Dougherty; K. E. Keller; D. Wang; R. O. Hampton
The common fig tree (Ficus carica L.) is a Mediterranean crop with problematic cultivar identification. The recovery and conservation of possible local varieties for ecological production requires the previous genetic characterization of the available germplasm. In this context, 42 lines corresponding to 12 local varieties and two caprifigs, in addition to 15 reference samples have been fingerprinted using 21 SSR markers. A total of 77 alleles were revealed, detecting a useful level of genetic variability within the local germplasm pools. UPGMA clustering analysis has revealed the genetic structure and relationships among the local and reference germplasm. Eleven of the local varieties could be identified and defined as obtained clusters, showing that SSR analysis is an efficient method to evaluate the Andalusian fig tree diversity for on-farm conservation. PMID:22804343
Perez-Jiménez, M; López, B; Dorado, G; Pujadas-Salvá, A; Guzmán, G; Hernandez, P
Bluetongue virus (BTV), a nonenveloped insect-borne virus, is released from infected cells by multiple pathways. Unlike other nonenveloped viruses, in addition to cell lysis the newly synthesized virus particles also appear to use a unique “budding” process. The nonstructural protein NS3, the only membrane protein encoded by BTV in infected cells, has been implicated in this process, since it appears to interact not only with the outermost viral capsid protein VP2 but also with a component of the cellular ESCRT pathway. However, to date it had not been possible to obtain direct evidence for the involvement of NS3 in BTV morphogenesis due to the lack of a genetic system that would allow introducing the targeted mutation in NS3 gene. In this study, we have used the recently developed T7 transcript-based reverse genetics system for BTV to introduce mutations in the sequence of NS3 into the viral genome and have investigated the effect of these mutations in the context of a replicating virus. While certain NS3 mutations exhibited drastic effects on newly synthesized virus release, others had less pronounced effects. In particular, mutations of two residues in the Tsg101 binding motif, the putative L domain of NS3, altered normal virus egress patterns and left nascent particles tethered to the cellular membrane, apparently arrested in the process of budding. In cells infected with a mutant virus that was incapable of an NS3-VP2 interaction, no budding particles were visualized. These data suggest that NS3 may act like the membrane protein of enveloped viruses and is responsible for intracellular trafficking and budding of virus particles. NS3 is thus a bridge between the maturing virion particles and cellular proteins during virus egress.
Celma, Cristina C. P.; Roy, Polly
Preface New technologies have widened our view of “complex diseases”--diseases with both genetic and environmental risk factors. Here, we explore recent genetic and virologic evidence implicating host-virus interactions in three diseases—type 1 diabetes, inflammatory bowel disease, and asthma. In these examples, the viruses implicated in disease are mucosal infections that affect most of the population and that are asymptomatic or mild in many hosts. These findings place a new emphasis on common viral infections as an important environmental factor in complex disease pathogenesis, and they compel us to pursue a better understanding of host interactions with the human virome.
Foxman, Ellen F.; Iwasaki, Akiko
Genetic engineering of forest tree species is regarded as a strategy to reduce worldwide pressure on natural forests, to conserve\\u000a genetic resources and ameliorate stress on global climate, and to meet growing demand for forest wood and timber products.\\u000a Genetic engineering approaches toward the control or management of fungal pathogens, arthropod herbivores, bacterial and viral\\u000a diseases, the use of pest
Tang Wei; Janet Ogbon; Aquilla McCoy
Background and AimsThe hepatitis C virus (HCV) invariably shows wide heterogeneity in infected patients, referred to as a quasispecies population. Massive amounts of genetic information due to the abundance of HCV variants could be an obstacle to evaluate the viral genetic heterogeneity in detail.MethodsUsing a newly developed massive-parallel ultra-deep sequencing technique, we investigated the viral genetic heterogeneity in 27 chronic
Akihiro Nasu; Hiroyuki Marusawa; Yoshihide Ueda; Norihiro Nishijima; Ken Takahashi; Yukio Osaki; Yukitaka Yamashita; Tetsuro Inokuma; Takashi Tamada; Takeshi Fujiwara; Fumiaki Sato; Kazuharu Shimizu; Tsutomu Chiba; Yoshio Yamaoka
Viral pathogens have been implicated in the development of certain cancers including human papillomavirus (HPV) in squamous cell carcinoma and Epstein-Barr virus (EBV) in Burkitt's lymphoma. The significance of viral pathogens in brain tumors is controversial, and human cytomegalovirus (HCMV) has been associated with glioblastoma (GBM) in some but not all studies, making the role of HCMV unclear. In this study we sought to determine if viral pathogen sequences could be identified in an unbiased manner from previously discarded, unmapped, non-human, next-generation sequencing (NGS) reads obtained from targeted oncology, panel-based sequencing of high grade gliomas (HGGs), including GBMs. Twenty one sequential HGG cases were analyzed by a targeted NGS clinical oncology panel containing 151 genes using DNA obtained from formalin-fixed, paraffin-embedded (FFPE) tissue. Sequencing reads that did not map to the human genome (average of 38,000 non-human reads/case (1.9%)) were filtered and low quality reads removed. Extracted high quality reads were then sequentially aligned to the National Center for Biotechnology Information (NCBI) non-redundant nucleotide (nt and nr) databases. Aligned reads were classified based on NCBI taxonomy database and all eukaryotic viral sequences were further classified into viral families. Two viral sequences (both herpesviruses), EBV and Roseolovirus were detected in 5/21 (24%) cases and in 1/21 (5%) cases, respectively. None of the cases had detectable HCMV. Of the five HGG cases with detectable EBV DNA, four had additional material for EBV in situ hybridization (ISH), all of which were negative for expressed viral sequence. Overall, a similar discovery approach using unmapped non-human NGS reads could be used to discover viral sequences in other cancer types. PMID:24704430
Cimino, Patrick J; Zhao, Guoyan; Wang, David; Sehn, Jennifer K; Lewis, James S; Duncavage, Eric J
Objective: To determine the personal characteristics and reasons associated with providing a buccal swab for apolipoprotein E (APOE) genetic testing in a primary care study. Methods: The study sample consisted of 342 adults aged 65 years and older recruited from primary care settings. Results: In all, 88% of patients agreed to provide a DNA sample for APOE genotyping and 78%
Hillary R. Bogner; Marsha N. Wittink; Jon F. Merz; Joseph B. Straton; Peter F. Cronholm; Peter V. Rabins; Joseph J. Gallo
This material includes instructional materials on the topics of DNA, genes, chromosomes, the cell cycle, mitosis, meiosis, gene expression, genetics and other related topics. Each topic contains a brief introduction that puts the teaching resources into context. This material has been written for students up to 18 years old and is continually revised to reflect changes and developments in the topic over time. Those topics include developmental genetics, DNA, legal issues, gene expression, and much more.
DNA vaccination (or genetic immunization) strategies provide important opportunities for improving immunization, since both humoral and cell-mediated responses are induced. The use of genetic vaccines for inducing immunity to infectious agents can eliminate or significantly alleviate the pathology associated with a broad range of infections. A requirement for efficient DNA vaccination is the development of gene delivery systems capable of overcoming barriers to gene transfection. Compared to viral systems, nonviral systems are considered to be safe, cheap, multiple delivery is possible and able to deliver larger pieces of DNA. Also, these nanocarriers avoid DNA degradation and facilitate targeted delivery to antigen presenting cells. This review describes the potential of non-viral nanocarrier construct(s) in genetic immunization. Issued patents in the field were retrieved from the US patent database. Various carrier systems used to deliver plasmid DNA were reviewed in detail. PMID:19075899
Khatri, Kapil; Goyal, Amit K; Vyas, Suresh P
Duck viral enteritis (DVE) outbreaks occurred at two different locations in Pennsylvania in 1991 and 1992. In the first outbreak, four ducks died out of a group of 30 domestic ducks; in the second outbreak, 65 ducks died out of a group of 114 domestic ducks, and 15 domestic geese died as well. A variety of species of ducks were present on both premises, but only muscovy ducks (Cairina moschata) died from the disease. On necropsy, gross lesions included hepatomegaly with petechial hemorrhages, petechial hemorrhages in the abdominal fat, petechial hemorrhages on the epicardial surface of the heart, and multifocal to coalescing areas of fibrinonecrotic material over the mucosal surface of the trachea, esophagus, intestine, and cloaca. Histologically, the liver had random multifocal areas of necrosis and eosinophilic intranuclear inclusion bodies in hepatocytes. DVE virus was isolated and identified using muscovy duck embryo fibroblast inoculation and virus neutralization. /// En dos sitios diferentes se presentaron brotes de enteritis viral de los patos en el estados de Pensilvania en los a??os 1991 y 1992. En el primer brote, cuatro de un lote de 30 patos murieron mientras que en el segundo brote murieron 65 patos de un lote de 114 patos y 15 gansos. En ambas localidades exist?-a una variedad de especies de patos, sin embargo, s??lamente los patos almizcleros (Cairina moschata) murieron. A la necropsia, las lesiones macrosc??picas incluyeron hepatomegalia con hemorragias petequiales, hemorragias petequiales en la grasa abdominal y en la superficie del epicardio, y ?!reas multifocales o coalescentes de material fibrinonecr??tico sobre la superficie de la mucosa de la tr?!quea, es??fago, intestino y cloaca. Histol??gicamente, el h?-gado mostraba ?!reas multifocales de necrosis y cuerpos de inclusi??n intranucleares eosinof?-licos en los hepatocitos. El virus de la enteritis viral de los patos fue aislado e identificado usando fibroblasto de embriones de pato almizclero y mediante la virus neutralizaci??n.
Davison, S.; Converse, K. A.; Hamir, A. N.; Eckroade, R. J.
Although there is some evidence on the usefulness of mobile viral marketing from marketers' perspective, little is known about the motivations, attitudes, and behaviors of consumers engaged in this marketing instrument. In this paper, we present the findings of a grounded theory study and focus on determining why a mobile viral effect occurs. The proposed framework helps researchers and marketers
Dietmar G. Wiedemann; Wolfgang Palka
Viral stealth marketing is a contemporary marketing technique, which has evolved in reaction to the increasingly competitive marketing environment. This paper notes that despite its huge potential, very little research is being targeted towards understanding the utility of viral stealth marketing, particularly in the context of Generation Y, whose behavioural characteristics are particularly suited to this form of marketing. This
Celeste Swanepoel; Ashley Lye; Robert Rugimbana
Human embryonic stem (ES) cells hold great promise for the study of human development and the generation of new therapeutic approaches to tissue regeneration and their genetic modification will play a key role in this development. While viral vectors have been readily used for gene transfer into human ES cells, only limited success has been achieved using non-viral vectors for
Andrew Wilber; Jonathan L. Linehan; Xinghui Tian; R. Scott McIvor; Dan S. Kaufman
The initiation of viral double stranded (ds) DNA replication involves proteins that recruit and load the replisome at the replication origin (ori). Any block in replication fork progression or a programmed barrier may act as a factor for ori-independent remodelling and assembly of a new replisome at the stalled fork. Then replication initiation becomes dependent on recombination proteins, a process called recombination-dependent replication (RDR). RDR, which is recognized as being important for replication restart and stability in all living organisms, plays an essential role in the replication cycle of many dsDNA viruses. The SPP1 virus, which infects Bacillus subtilis cells, serves as a paradigm to understand the links between replication and recombination in circular dsDNA viruses. SPP1-encoded initiator and replisome assembly proteins control the onset of viral replication and direct the recruitment of host-encoded replisomal components at viral oriL. SPP1 uses replication fork reactivation to switch from ori-dependent ?-type (circle-to-circle) replication to ?-type RDR. Replication fork arrest leads to a double strand break that is processed by viral-encoded factors to generate a D-loop into which a new replisome is assembled, leading to ?-type viral replication. SPP1 RDR proteins are compared with similar proteins encoded by other viruses and their possible in vivo roles are discussed. PMID:21708194
Lo Piano, Ambra; Martínez-Jiménez, María I; Zecchi, Lisa; Ayora, Silvia
For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development. PMID:22827378
Blackburn, H D
Alcoholism is a common disease resulting from the complex interaction of genetic, social, and environmental factors. Interest in the high heritability of alcoholism has resulted in many studies of how single genes, as well as an individual’s entire genetic content (i.e., genome) and the proteins expressed by the genome, influence alcoholism risk. The use of large-scale methods to identify and characterize genetic material (i.e., high-throughput technologies) for data gathering and analysis recently has made it possible to investigate the complexity of the genetic architecture of susceptibility to common diseases such as alcoholism on a systems level. Systems genetics is the study of all genetic variations, their interactions with each other (i.e., epistasis), their interactions with the environment (i.e., plastic reaction norms), their relationship with interindividual variation in traits that are influenced by many genes and contribute to disease susceptibility (i.e., intermediate quantitative traits or endophenotypes1) defined at different levels of hierarchical biochemical and physiological systems, and their relationship with health and disease. The goal of systems genetics is to provide an understanding of the complex relationship between the genome and disease by investigating intermediate biological processes. After investigating main effects, the first step in a systems genetics approach, as described here, is to search for gene–gene (i.e., epistatic) reactions.
Sloan, Chantel D.; Sayarath, Vicki; Moore, Jason H.
Background The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep Pyrosequencing (DPS) technology in combination with phenotypic experiments to analyze and compare with unprecedented detail the composition of viral isolates and in vivo quasispecies. Methodology/Principal Findings We amplified by DPS HIV-1 genomic regions covering gag, protease, integrase and env-V3 to characterize paired isolates from plasma and peripheral blood mononuclear cells and compare them with total plasma viral RNA in four recently HIV-1 infected subjects. Our study demonstrated the presence of unique haplotypes scattered between sample types with conservation of major variants. In addition, no differences in intra- and inter-population encoded protein variability were found between the different types of isolates or when these were compared to plasma viral RNA within subjects. Additionally, in vitro experiments demonstrated phenotypic similarities in terms of replicative capacity and co-receptor usage between viral isolates and plasma viral RNA. Conclusion This study is the first in-depth comparison and characterization of viral isolates from different sources and plasma circulating quasispecies using DPS in recently HIV-1 infected subjects. Our data supports the use of primary isolates regardless of their plasma or cellular origin to define genetic variability and biological traits of circulating HIV-1 quasispecies.
Erkizia, Itziar; Pino, Maria; Pou, Christian; Paredes, Roger; Clotet, Bonaventura; Martinez-Picado, Javier; Prado, Julia G.
Dynein light chains mediate the interaction between the cargo and the dynein motor complex during retrograde microtubule-mediated transport in eukaryotic cells. In this study, we expressed and characterized the recombinant human dynein light chain Rp3 and developed a modified variant harboring an N-terminal DNA-binding domain (Rp3-Db). Our approach aimed to explore the retrograde cell machinery based on dynein to enhance plasmid DNA (pDNA) traffic along the cytosol toward the nucleus. In the context of non-viral gene delivery, Rp3-Db is expected to simultaneously interact with DNA and dynein, thereby enabling a more rapid and efficient transport of the genetic material across the cytoplasm. We successfully purified recombinant Rp3 and obtained a low-resolution structural model using small-angle X-ray scattering. Additionally, we observed that Rp3 is a homodimer under reducing conditions and remains stable over a broad pH range. The ability of Rp3 to interact with the dynein intermediate chain in vitro was also observed, indicating that the recombinant Rp3 is correctly folded and functional. Finally, Rp3-Db was successfully expressed and purified and exhibited the ability to interact with pDNA and mediate the transfection of cultured HeLa cells. Rp3-Db was also capable of interacting in vitro with dynein intermediate chains, indicating that the addition of the N-terminal DNA-binding domain does not compromise its function. The transfection level observed for Rp3-Db is far superior than that reported for protamine and is comparable to that of the cationic lipid Lipofectamine™. This report presents an initial characterization of a non-viral delivery vector based on the dynein light chain Rp3 and demonstrates the potential use of modified human light chains as gene delivery vectors. PMID:24077724
Toledo, M A S; Favaro, M T P; Alves, R F; Santos, C A; Beloti, L L; Crucello, A; Santiago, A S; Mendes, J S; Horta, M A C; Aparicio, R; Souza, A P; Azzoni, A R
Distinct roadblocks prevent translating basic findings in viral pathogenesis into therapies and implementing potential solutions in the clinic. An ongoing partnership between the Volkswagen Foundation and Nature Medicine resulted in an interactive meeting in 2012, as part of the "Herrenhausen Symposia" series. Current challenges for various fields of viral research were recognized and discussed with a goal in mind--to identify solutions and propose an agenda to address the translational barriers. Here, some of the researchers who participated at the meeting provide a concise outlook at the most pressing unmet research and clinical needs, identifying these key obstacles is a necessary step towards the prevention and cure of human viral diseases. PMID:23296014
Deeks, Steven; Drosten, Christian; Picker, Louis; Subbarao, Kanta; Suzich, Joann
OBJECTIVE To determine the personal characteristics and reasons associated with providing a buccal swab for APOE genetic testing in a primary care study. METHODS The study sample consisted of 342 adults aged 65 years and older recruited from primary care settings. RESULTS In all, 88% of patients agreed to provide a DNA sample for APOE genotyping and 78% of persons providing a sample agreed to banking of the DNA. Persons aged 80 years and older and African-Americans were less likely to participate in APOE genotyping. Concern about confidentiality was the most common reason for not wanting to provide a DNA sample or to have DNA banked. CONCLUSION We found stronger relationships between sociodemographic variables of age and ethnicity with participation in genetic testing than we did between level of educational attainment, gender, function, cognition, and affect.
Bogner, Hillary R.; Wittink, Marsha N.; Merz, Jon F.; Straton, Joseph B.; Cronholm, Peter F.; Rabins, Peter V.; Gallo, Joseph J.
The interferon-inducible transmembrane (IFITM) protein family represents a new class of cellular restriction factors that block early stages of viral replication; the underlying mechanism is currently not known. Here we provide evidence that IFITM proteins restrict membrane fusion induced by representatives of all three classes of viral membrane fusion proteins. IFITM1 profoundly suppressed syncytia formation and cell-cell fusion induced by almost all viral fusion proteins examined; IFITM2 and IFITM3 also strongly inhibited their fusion, with efficiency somewhat dependent on cell types. Furthermore, treatment of cells with IFN also markedly inhibited viral membrane fusion and entry. By using the Jaagsiekte sheep retrovirus envelope and influenza A virus hemagglutinin as models for study, we showed that IFITM-mediated restriction on membrane fusion is not at the steps of receptor- and/or low pH-mediated triggering; instead, the creation of hemifusion was essentially blocked by IFITMs. Chlorpromazine (CPZ), a chemical known to promote the transition from hemifusion to full fusion, was unable to rescue the IFITM-mediated restriction on fusion. In contrast, oleic acid (OA), a lipid analog that generates negative spontaneous curvature and thereby promotes hemifusion, virtually overcame the restriction. To explore the possible effect of IFITM proteins on membrane molecular order and fluidity, we performed fluorescence labeling with Laurdan, in conjunction with two-photon laser scanning and fluorescence-lifetime imaging microscopy (FLIM). We observed that the generalized polarizations (GPs) and fluorescence lifetimes of cell membranes expressing IFITM proteins were greatly enhanced, indicating higher molecularly ordered and less fluidized membranes. Collectively, our data demonstrated that IFITM proteins suppress viral membrane fusion before the creation of hemifusion, and suggested that they may do so by reducing membrane fluidity and conferring a positive spontaneous curvature in the outer leaflets of cell membranes. Our study provides novel insight into the understanding of how IFITM protein family restricts viral membrane fusion and infection.
Golfetto, Ottavia; Bungart, Brittani; Li, Minghua; Ding, Shilei; He, Yuxian; Liang, Chen; Lee, James C.; Gratton, Enrico; Cohen, Fredric S.; Liu, Shan-Lu
Gene annotation in viruses often relies upon similarity search methods. These methods possess high specificity but some genes may be missed, either those unique to a particular genome or those highly divergent from known homologs. To identify potentially missing viral genes we have analyzed all complete viral genomes currently available in GenBank with a specialized and augmented version of the gene finding program GeneMarkS. In particular, by implementing genome-specific self-training protocols we have better adjusted the GeneMarkS statistical models to sequences of viral genomes. Hundreds of new genes were identified, some in well studied viral genomes. For example, a new gene predicted in the genome of the Epstein–Barr virus was shown to encode a protein similar to ?-herpesvirus minor tegument protein UL14 with heat shock functions. Convincing evidence of this similarity was obtained after only 12 PSI-BLAST iterations. In another example, several iterations of PSI-BLAST were required to demonstrate that a gene predicted in the genome of Alcelaphine herpesvirus 1 encodes a BALF1-like protein which is thought to be involved in apoptosis regulation and, potentially, carcinogenesis. New predictions were used to refine annotations of viral genomes in the RefSeq collection curated by the National Center for Biotechnology Information. Importantly, even in those cases where no sequence similarities were detected, GeneMarkS significantly reduced the number of primary targets for experimental characterization by identifying the most probable candidate genes. The new genome annotations were stored in VIOLIN, an interactive database which provides access to similarity search tools for up-to-date analysis of predicted viral proteins.
Mills, Ryan; Rozanov, Michael; Lomsadze, Alexandre; Tatusova, Tatiana; Borodovsky, Mark
Latent viruses are ubiquitous and reactivate during stressful periods with and without symptoms. Latent herpes virus reactivation is used as a tool to predict changes in the immune status in astronauts and to evaluate associated health risks. Methods: Viral DNA was detected by real time polymerase chain reaction in saliva and urine from astronauts before, during and after short and long-duration space flights. Results and Discussion: EpsteinBarr virus (EBV), cytomegalovirus (CMV), and varicella zoster virus (VZV) reactivated, and viral DNA was shed in saliva (EBV and VZV) or urine (CMV). EBV levels in saliva during flight were 10fold higher than baseline levels. Elevations in EBV specific CD8+ T-cells, viral antibody titers, and specific cytokines were consistent with viral reactivation. Intracellular levels of cytokines were reduced in EBVspecific Tcells. CMV, rarely present in urine of healthy individuals, was shed in urine of 27% of astronauts during all phases of spaceflight. VZV, not found in saliva of asymptomatic individuals, was found in saliva of 50% of astronauts during spaceflight and 35 days after flight. VZV recovered from astronaut saliva was found to be live, infectious virus. DNA sequencing demonstrated that the VZV recovered from astronauts was from the common European strain of VZV. Elevation of stress hormones accompanied viral reactivation indicating involvement of the hypothalmic-pituitary-adrenal and sympathetic adrenal-medullary axes in the mechanism of viral reactivation in astronauts. A study of 53 shingles patients found that all shingles patients shed VZV DNA in their saliva and the VZV levels correlated with the severity of the disease. Lower VZV levels in shingles patients were similar to those observed in astronauts. We proposed a rapid, simple, and cost-effective assay to detect VZV in saliva of patients with suspected shingles. Early detection of VZV infection allows early medical intervention.
Pierson, D. L.; Mehta, S. K.; Stowe, R.
The disease Xeroderma Pigmentosum (XP) is genetically heterogeneous and defined by pathogenic variants (formerly termed mutations) in any of eight different genes. Pathogenic variants in the XPC gene are the most commonly observed in US patients. Moreover, pathogenic variants in just four of the genes, XPA, XPC, XPD\\/ERCC2 and XPV\\/POLH account for 91% of all XP cases worldwide. In the
Amanda Rivera-Begeman; Lisa D. McDaniel; Roger A. Schultz; Errol C. Friedberg
Picornaviruses cause several diseases, not only in humans but also in various animal hosts. For instance, human enteroviruses can cause hand-foot-and-mouth disease, herpangina, myocarditis, acute flaccid paralysis, acute hemorrhagic conjunctivitis, severe neurological complications, including brainstem encephalitis, meningitis and poliomyelitis, and even death. The interaction between the virus and the host is important for viral replication, virulence and pathogenicity. This article reviews studies of the functions of viral and host factors that are involved in the life cycle of picornavirus. The interactions of viral capsid proteins with host cell receptors is discussed first, and the mechanisms by which the viral and host cell factors are involved in viral replication, viral translation and the switch from translation to RNA replication are then addressed. Understanding how cellular proteins interact with viral RNA or viral proteins, as well as the roles of each in viral infection, will provide insights for the design of novel antiviral agents based on these interactions. PMID:19925687
Lin, Jing-Yi; Chen, Tzu-Chun; Weng, Kuo-Feng; Chang, Shih-Cheng; Chen, Li-Lien; Shih, Shin-Ru
We studied 80 hepatocellular carcinomas from three continents for p53 gene (TP53) mutations and hepatitis B virus (HBV) sequences. p53 mutations were frequent in tumors from Mozambique but not in tumors from South Africa, China, and Germany. Independent of geographic origin, most tumors were positive for HBV sequences. X gene coding sequences of HBV were detected in 78% of tumors, whereas viral sequences in the surface antigen- and core antigen-encoding regions were present in less than 45% of tumors. These observations indicate that hepatocellular carcinomas are genetically heterogeneous. Mozambican-type of hepatocellular carcinomas are characterized by a high incidence of p53 mutations related to aflatoxins. In other tumors, the rarity of p53 mutations combined with the frequent presence of viral X gene coding sequences suggests a possible interference of HBV with the wild-type p53 function.
Unsal, H; Yakicier, C; Marcais, C; Kew, M; Volkmann, M; Zentgraf, H; Isselbacher, K J; Ozturk, M
The authors studied 80 hepatocellular carcinomas from three continents for p53 gene (TP53) mutations and hepatitis B virus (HBV) sequences. p53 mutations were frequent in tumors from Mozambique but not in tumors from South Africa, China, and Germany. Independent of geographic origin, most tumors were positive for HBV sequences. X gene coding sequences of HBV were detected in 78% of tumors, whereas viral sequences in the surface antigen- and core antigen-encoding regions were present in less than 35% of tumors. These observations indicate that hepatocellular carcinomas are genetically heterogeneous. Mozambican-types of hepatocellular carcinomas are characterized by a high incidence of p53 mutations related to aflatoxins. In other tumors, the rarity of p53 mutations combined with the frequent presence of viral X gene coding sequences suggests a possible interference of HBV with the wild-type p53 function.
Unsal, H.; Isselbacher, K.J. (Massachusetts General Hospital Cancer Center, Charlestown, MA (United States)); Yakicier, C.; Marcais, C.; Ozturk, M. (Institut National de la Sante et de la Recherche Medicale, Lyon (France)); Kew, M. (Univ. of Witwatersrand, Johannesburg (South Africa)); Volkmann, M. (Univ. of Heidelberg (Germany)); Zentgraf, H. (Deutsches Krebsforschungszentrum, Heidelberg (Germany))
Human immunodeficiency virus type 2 (HIV-2) is much less pathogenic than HIV-1, and HIV-2 infection is associated with plasma viral loads significantly lower than those found in HIV-1 infection. We have developed a real-time quantitative PCR method for measuring the HIV-2 RNA load that covers the range of genetic diversity of HIV-2 isolates and that detects extremely low viral loads. Samples from 49 patients were studied. Proviral DNA was first detected and quantified. The strains that were detected were then genotyped: 21 patients were infected with HIV-2 subtype A and 15 patients were infected with HIV-2 subtype B; 1 patient was infected with a highly divergent strain. Env PCR failed for the remaining 12 patients, so subtypes could not be determined. For viral RNA quantification, a stock of HIV-2 strain NIHZ, which was counted by electron microscopy, was used as the standard. Several primer sets targeting the highly conserved gag region were evaluated. Various primer combinations failed to amplify subtype B strains. With the final primer pair selected, which detected both subtype A and subtype B strains, the sensitivity of the assay was 100% at a viral load of 250 copies/ml and 66% at a viral load of 125 copies/ml. We found a correlation between the CD4+-cell count, the clinical stage, and the plasma HIV-2 RNA level. The median plasma HIV-2 RNA value for the 33 asymptomatic patients was 2.14 log10, whereas it was 3.1 log10 for the 16 patients with AIDS (P < 0.01). Proviral DNA was detectable in 18 symptom-free patients with high CD4+-cell counts, in whom viral RNA was undetectable.
Damond, Florence; Gueudin, Marie; Pueyo, Sophie; Farfara, Isabelle; Robertson, David L.; Descamps, Diane; Chene, Genevieve; Matheron, Sophie; Campa, Pauline; Brun-Vezinet, Francoise; Simon, Francois
Human immunodeficiency virus type 2 (HIV-2) is much less pathogenic than HIV-1, and HIV-2 infection is associated with plasma viral loads significantly lower than those found in HIV-1 infection. We have developed a real-time quantitative PCR method for measuring the HIV-2 RNA load that covers the range of genetic diversity of HIV-2 isolates and that detects extremely low viral loads. Samples from 49 patients were studied. Proviral DNA was first detected and quantified. The strains that were detected were then genotyped: 21 patients were infected with HIV-2 subtype A and 15 patients were infected with HIV-2 subtype B; 1 patient was infected with a highly divergent strain. Env PCR failed for the remaining 12 patients, so subtypes could not be determined. For viral RNA quantification, a stock of HIV-2 strain NIHZ, which was counted by electron microscopy, was used as the standard. Several primer sets targeting the highly conserved gag region were evaluated. Various primer combinations failed to amplify subtype B strains. With the final primer pair selected, which detected both subtype A and subtype B strains, the sensitivity of the assay was 100% at a viral load of 250 copies/ml and 66% at a viral load of 125 copies/ml. We found a correlation between the CD4(+)-cell count, the clinical stage, and the plasma HIV-2 RNA level. The median plasma HIV-2 RNA value for the 33 asymptomatic patients was 2.14 log(10), whereas it was 3.1 log(10) for the 16 patients with AIDS (P < 0.01). Proviral DNA was detectable in 18 symptom-free patients with high CD4(+)-cell counts, in whom viral RNA was undetectable. PMID:12354861
Damond, Florence; Gueudin, Marie; Pueyo, Sophie; Farfara, Isabelle; Robertson, David L; Descamps, Diane; Chène, Geneviève; Matheron, Sophie; Campa, Pauline; Brun-Vézinet, Françoise; Simon, François
Phosphorylation represents one the most abundant and important posttranslational modifications of proteins, including viral proteins. Virus-encoded serine/threonine protein kinases appear to be a feature that is unique to large DNA viruses. Although the importance of these kinases for virus replication in cell culture is variable, they invariably play important roles in virus virulence. The current review provides an overview of the different viral serine/threonine protein kinases of several large DNA viruses and discusses their function, importance, and potential as antiviral drug targets.
Jacob, Thary; Van den Broeke, Celine; Favoreel, Herman W.
\\u000a Key Principles\\u000a \\u000a Chronic hepatitis B and C are the most common etiological factors worldwide for cirrhosis and hepatocellular carcinoma (HCC).\\u000a \\u000a \\u000a Liver transplantation (LT) is the only option for those with complicated cirrhosis and early HCC.\\u000a \\u000a \\u000a Outcomes of LT for viral hepatitis are compromised by recurrent viral infection, resulting in allograft failure.\\u000a \\u000a \\u000a Combined passive immunoprophylaxis and the use of oral antiviral
In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions. PMID:16800884
Resnik, David B; Vorhaus, Daniel B
In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.
Resnik, David B; Vorhaus, Daniel B
Aquaculture has expanded rapidly to become a major economic and food-producing sector worldwide these last 30 years. In parallel, viral diseases have emerged and rapidly spread from farm to farm causing enormous economic losses. The most problematic viruses encountered in the field are mainly, but not exclusively, RNA viruses belonging to the Novirhabdovirus, Aquabirnavirus, Alphavirus and Betanodavirus genera. The recent establishment of reverse genetics systems to recover infectious fish RNA viruses entirely from cDNA has made possible to genetically manipulate the viral genome. These systems have provided powerful tools to study all aspects of the virus biology and virus-host interactions but also gave the opportunity to use these viruses as live vaccines or as gene vectors. This review provides an overview on the recent breakthroughs achieved by using these reverse genetics systems in terms of viral protein function, virulence and host-specificity factor, vaccine development and vector design.
Aquaculture has expanded rapidly to become a major economic and food-producing sector worldwide these last 30 years. In parallel, viral diseases have emerged and rapidly spread from farm to farm causing enormous economic losses. The most problematic viruses encountered in the field are mainly, but not exclusively, RNA viruses belonging to the Novirhabdovirus, Aquabirnavirus, Alphavirus and Betanodavirus genera. The recent establishment of reverse genetics systems to recover infectious fish RNA viruses entirely from cDNA has made possible to genetically manipulate the viral genome. These systems have provided powerful tools to study all aspects of the virus biology and virus-host interactions but also gave the opportunity to use these viruses as live vaccines or as gene vectors. This review provides an overview on the recent breakthroughs achieved by using these reverse genetics systems in terms of viral protein function, virulence and host-specificity factor, vaccine development and vector design. PMID:21314978
Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.
Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.
The mosaic of environment involvement in autoimmunity: the abrogation of viral latency by stress, a non-infectious environmental agent, is an intrinsic prerequisite prelude before viruses can rank as infectious environmental agents that trigger autoimmune diseases.
An autoimmune disease (AD), organ-specific or systemic, results from an aberrant response in which the protective immune system normally schooled to recognize and destroy invading infectious agents (viruses, etc.) instead fails to distinguish self-antigens and proceeds to attack and destroy the host's organs. There can be familial aggregation in which a single AD may occur in members of a family, or a single family may be afflicted with multiple ADs. Finally, sometimes multiple ADs co-occur in a single individual: the kaleidoscope of autoimmunity. Autoimmunity is a multifactorial process in which genetic, hormonal, immunological and environmental factors act in concert to materialize the mosaic of autoimmunity phenomenon. A genetically primed individual may yet not develop an AD: the contribution by an environmental factor (non-infectious or infectious) is essential for completion of the act. Of the non-infectious factors, stress plays a determinative step in autoimmunity in that it abrogates viral latency and thereby ordains the viruses to qualify as infectious environmental factors that trigger ADs. This is note-worthy as viruses rank first as the most important environmental triggers of ADs. Furthermore, all these viruses experience going through latency. Hence the hypothesis: "The abrogation of viral latency by stress, a non-infectious environmental agent, is an intrinsic prerequisite prelude before viruses can rank as infectious environmental agents that trigger autoimmune diseases". There is collaboration here between non-infectious- and infectious-agent to achieve the cause of autoimmunity. We say viral latency and stress have a covenant: continued perpetration of autoimmunity is dependent on the intervention by stress to reactivate latent infections. PMID:24418293
Temajo, Norbert O; Howard, Neville
Intranasal application of vesicular stomatitis virus (VSV) induces acute encephalitis characterized by a pronounced myeloid and T cell infiltrate. The role of distinct phagocytic populations on VSV encephalitis was therefore examined in this study. Ablation of peripheral macrophages did not impair VSV encephalitis or viral clearance from the brain, whereas, depletion of splenic marginal dendritic cells impaired this response and enhanced morbidity/mortality. Selective depletion of brain perivascular macrophages also suppressed this response without altering viral clearance. Thus, two anatomically distinct phagocytic populations regulate VSV encephalitis in a non-redundant fashion although neither population is essential for viral clearance in the CNS.
Steel, Christina D.; Kim, Woong-Ki; Sanford, Larry; Wellman, Laurie; Burnett, Sandra; Van Rooijen, Nico; Ciavarra, Richard P.
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F2408 rat cells transformed by polyoma virus contained integrated and nonintegrated viral DNA. The presence of nonintegrated viral DNA is under control of the A early viral function. Polyoma ts-a-transformed rat cells lose the free viral DNA when growth at the nonpermissive temperature (40 degrees C), but they reexpress it 1 to 3 days after they are shifted back to the permissive temperature. In contrast, rat cells transformed by a late viral mutant, ts-8, contain free viral DNA at both permissive and nonpermissive temperatures. Treatment of the transformed rat cells with mitomycin C produces a large increase in the quantity of free viral DNA and some production of infectious virus. Experiments of in situ hybridization, with 3H-labeled polyoma complementary RNA as a probe, show that only a minority (approximately 0.1%) of the transformed cells contain nonintegrated viral DNA at any given time. These results suggest that the presence of free viral DNA in polyoma-transformed rat cells is caused by a spontaneous induction of viral DNA replication, occurring with low but constant probability in the transformed cell population, and that the free viral DNA molecules originate from the integrated ones, probably through a phenomenon of excision and limited replication. Images
Zouzias, D; Prasad, I; Basilico, C
Many viruses, including bovine herpesvirus-1 (BHV-1), bovine respiratory syncytial virus (BRSV), parainfluenzavirus-3 (PI3), bovine coronavirus, bovine viral diarrhea virus and bovine reovirus, have been etiologically associated with respiratory disease in cattle. This review focuses on the pathogenesis of BHV-1 and BRSV, two very different agents that primarily cause disease in the upper and lower respiratory tract, respectively. PMID:20003652
Ellis, John A
Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common
Mya Breitbart; Peter Salamon; Bjarne Andresen; Joseph M. Mahaffy; Anca M. Segall; David Mead; Farooq Azam; Forest Rohwer
Based on the observation that viral infection results in the presentation of virus-specific peptides in association with both MHC Class I and MHC Class II on the surface of infected cells, strategies have been designed to use recombinant viruses carrying tumour-associated antigen (TAA) genes as immunization vehicles to elicit tumour-specific immune responses. I report here on results from phase I clinical studies based on a canarypox viral vector system expressing TAAs of interest. Clinical studies conducted in patients with colorectal cancer to evaluate ALVAC-CEA, ALVAC-KSA, or ALVAC-p53 candidate vaccines have shown that this approach is safe and can induce tumour-specific responses. Additional clinical studies evaluating candidate vaccines against melanoma, targeting either the gp100, Mage 1 or Mage 3 molecules are in progress. On the basis of our results and in the context of parallel studies being conducted with other viral systems, the characteristics of an ideal viral vector system, as it applies to therapeutic cancer vaccination, are discussed. PMID:15603188
Airway viral infections are associated with the pathogenesis of asthma and COPD. It has been argued that respiratory syncytial virus (RSV) infection in infancy is a probable causal factor in the development of pediatric asthma. RSV infections tend to induce Th2-biased immune responses in the host airways. RSV infection, atopy, and low pulmonary function in neonates may work synergistically toward the development of pediatric asthma. Human rhinovirus (HRV) is a representative virus associated with the exacerbation of asthma in both children and adults. Viral infections trigger innate immune responses including granulocytic inflammation and worsen the underlying inflammation due to asthma and COPD. The innate immune responses involve type-I and -III interferon (IFN) production, which plays an important role in anti-viral responses, and the airway epithelia of asthmatics reportedly exhibit defects in the virus-induced IFN responses, which renders these individuals more susceptible to viral infection. A similarly impaired IFN response is seen in COPD, and several investigators propose that latent adenoviral infection may be involved in COPD development. Persistent RSV infections were detected in a sub-population of patients with COPD and were associated with the accelerated decline of lung function. The virus-induced upregulation of co-inhibitory molecules in the airway epithelium partly accounts for the persistent infections. Experimental animal models for virus-asthma/COPD interactions have shed light on the underlying immune mechanisms and are expected to help develop novel approaches to treat respiratory diseases. PMID:24636264
Matsumoto, Koichiro; Inoue, Hiromasa
Hepatitis B is a DNA virus that infects liver cells and can cause both acute and chronic disease. It is believed that both viral and host factors are responsible for determining whether the infection is cleared or becomes chronic. Here we investigate the mechanism of protection by developing a mathematical model of the antibody response following hepatitis B virus (HBV) infection. We fitted the model to data from seven infected adults identified during acute infection and determined the ability of the virus to escape neutralization through overproduction of non-infectious subviral particles, which have HBs proteins on their surface, but do not contain nucleocapsid protein and viral nucleic acids. We showed that viral clearance can be achieved for high anti-HBV antibody levels, as in vaccinated individuals, when: (1) the rate of synthesis of hepatitis B subviral particles is slow; (2) the rate of synthesis of hepatitis B subviral particles is high but either anti-HBV antibody production is fast, the antibody affinity is high, or the levels of pre-existent HBV-specific antibody at the time of infection are high, as could be attained by vaccination. We further showed that viral clearance can be achieved for low equilibrium anti-HBV antibody levels, as in unvaccinated individuals, when a strong cellular immune response controls early infection. PMID:25078553
Ciupe, Stanca M; Ribeiro, Ruy M; Perelson, Alan S
The purpose of this review is to analyze the role of reactive oxygen species (ROS) in the pathogenesis of viral infections, an area of research that has recently gained momentum given the accumulation of evidence regarding the role of ROS in the pathogenesis of infection with the human immunodeficiency virus (HIV). Attention will be focussed on three classes of viruses:
Kathleen B. Schwarz
Survivors of meningitis often complain about neurological and neuropsychological consequences. In this study, the extent of these sequelae was quantified and correlated to MRI findings. Neurological, neuropsychological and neuroradiological examinations were performed with adultpatientsyounger than 70years, 1-12yearsafter recovery from bacterial meningitis (BM; n = 59), or from viral meningitis (VM; n = 59). Patients with other potential causes for neuropsychological
H. Schmidt; B. Heimann; M. Djukic; C. Mazurek; C. Fels; C.-W. Wallesch; R. Nau
Acute encephalitis constitutes a medical emergency. In most cases, the presence of focal neurological signs and focal seizures will distinguish encephalitis from encephalopathy. Acute disseminated encephalomyelitis is a non-infective inflammatory encephalitis that may require to be treated with steroids. Acute infective encephalitis is usually viral. Herpes simplex encephalitis (HSE) is the commonest sporadic acute viral encephalitis in the Western world. Magnetic resonance imaging of brain is the investigation of choice in HSE and the diagnosis may be confirmed by the polymerase chain reaction test for the virus in the cerebrospinal fluid. In this article, we review the diagnosis, investigations, and management of acute encephalitis. With few exceptions (for example, aciclovir for HSE), no specific therapy is available for most forms of viral encephalitis. Mortality and morbidity may be high and long term sequelae are known among survivors. The emergence of unusual forms of zoonotic encephalitis has posed an important public health problem. Vaccination and vector control measures are