Targeting Cell Cycle Facilitates E1A-Independent Adenoviral Replication

DNA replication of E1-deleted first-generation adenoviruses (AdV) in cultured cancer cells has been reported repeatedly and it was suggested that certain cellular proteins could functionally compensate for E1A, leading to the expression of the early region 2 (E2)-encoded proteins and subsequently virus replication. Referring to this, the observation was named E1A-like activity. In this study, we investigated different cell cycle inhibitors with respect to their ability to increase viral DNA replication of dl70-3, an E1-deleted adenovirus. Our analyses of this issue revealed that in particular inhibition of cyclin-dependent kinases 4/6 (CDK4/6i) increased E1-independent adenovirus E2-expression and viral DNA replication. Detailed analysis of the E2-expression in dl70-3 infected cells by RT-qPCR showed that the increase in E2-expression originated from the E2-early promoter. Mutations of the two E2F-binding sites in the E2-early promoter (pE2early-LucM) caused a significant reduction in E2-early promoter activity in trans-activation assays. Accordingly, mutations of the E2F-binding sites in the E2-early promoter in a virus named dl70-3/E2Fm completely abolished CDK4/6i induced viral DNA replication. Thus, our data show that E2F-binding sites in the E2-early promoter are crucial for E1A independent adenoviral DNA replication of E1-deleted vectors in cancer cells. IMPORTANCE E1-deleted AdV vectors are considered replication deficient and are important tools for the study of virus biology, gene therapy, and large-scale vaccine development. However, deletion of the E1 genes does not completely abolish viral DNA replication in cancer cells. Here, we report, that the two E2F-binding sites in the adenoviral E2-early promoter contribute substantially to the so-called E1A-like activity in tumor cells. With this finding, on the one hand, the safety profile of viral vaccine vectors can be increased and, on the other hand, the oncolytic property for cancer therapy might be improved through targeted manipulation of the host cell.

A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV

To study viral evolutionary processes within patients, mathematical models have been instrumental. Yet, the need for stochastic simulations of minority mutant dynamics can pose computational challenges, especially in heterogeneous systems where very large and very small sub-populations coexist. Here, we describe a hybrid stochastic-deterministic algorithm to simulate mutant evolution in large viral populations, such as acute HIV-1 infection, and further include the multiple infection of cells. We demonstrate that the hybrid method can approximate the fully stochastic dynamics with sufficient accuracy at a fraction of the computational time, and quantify evolutionary end points that cannot be expressed by deterministic models, such as the mutant distribution or the probability of mutant existence at a given infected cell population size. We apply this method to study the role of multiple infection and intracellular interactions among different virus strains (such as complementation and interference) for mutant evolution. Multiple infection is predicted to increase the number of mutants at a given infected cell population size, due to a larger number of infection events. We further find that viral complementation can significantly enhance the spread of disadvantageous mutants, but only in select circumstances: it requires the occurrence of direct cell-to-cell transmission through virological synapses, as well as a substantial fitness disadvantage of the mutant, most likely corresponding to defective virus particles. This, however, likely has strong biological consequences because defective viruses can carry genetic diversity that can be incorporated into functional virus genomes via recombination. Through this mechanism, synaptic transmission in HIV might promote virus evolvability.

The evolution of human immunodeficiency virus within patients is an important part of the disease process. In particular, the presence of mutants that are resistant against anti-viral drugs can result in challenges to the long-term control of the infection. To study disease progression, computer simulations have been useful. However, in some cases these simulations can be difficult because of the complexity of the model. Here, we use a computational complexity reducing algorithm to simulate mutant dynamics in large populations, which can approximate the full model at a fraction of the time. The use of this algorithm allows us to study different transmission methods, viral processes that occur between virus strains within individual cells, and important quantities such as the mutant distribution or the probability of mutant existence at a given infected cell population size. We find that the direct synaptic cell-to-cell transmission of the virus through virological synapses can have strong biological consequences because it can promote potentially defective viruses that carry genetic diversity which can be incorporated into functional virus genomes during infection. Through this process, synaptic transmission in human immunodeficiency virus might promote virus evolvability.

Modeling Hepatotropic Viral Infections: Cells vs. Animals

The lack of an appropriate platform for a better understanding of the molecular basis of hepatitis viruses and the absence of reliable models to identify novel therapeutic agents for a targeted treatment are the two major obstacles for launching efficient clinical protocols in different types of viral hepatitis. Viruses are obligate intracellular parasites, and the development of model systems for efficient viral replication is necessary for basic and applied studies. Viral hepatitis is a major health issue and a leading cause of morbidity and mortality. Despite the extensive efforts that have been made on fundamental and translational research, traditional models are not effective in representing this viral infection in a laboratory. In this review, we discuss in vitro cell-based models and in vivo animal models, with their strengths and weaknesses. In addition, the most important findings that have been retrieved from each model are described.

From cellular function to global impact: the vascular perspective on COVID-19

Since COVID-19 was declared a pandemic a year ago, our understanding of its effects on the vascular system has slowly evolved. At the cellular level, SARS-CoV-2 - the virus that causes COVID-19 - accesses the vascular endothelium through the angiotensin-converting enzyme 2 (ACE-2) receptor and induces proinflammatory and prothrombotic responses. At the clinical level, these pathways lead to thromboembolic events that affect the pulmonary, extracranial, mesenteric, and lower extremity vessels. At the population level, the presence of vascular risk factors predisposes individuals to more severe forms of COVID-19, whereas the absence of vascular risk factors does not spare patients with COVID-19 from unprecedented rates of stroke, pulmonary embolism and acute limb ischemia. Finally, at the community and global level, the fear of COVID-19, measures taken to limit the spread of SARS-CoV-2 and reallocation of limited hospital resources have led to delayed presentations of severe forms of ischemia, surgery cancellations and missed opportunities for limb salvage. The purpose of this narrative review is to present some of the data on COVID-19, from cellular mechanisms to clinical manifestations, and discuss its impact on the local and global surgical communities from a vascular perspective.

Viral cell-to-cell spread: Conventional and non-conventional ways

A critical step in the life cycle of a virus is spread to a new target cell, which generally involves the release of new viral particles from the infected cell which can then initiate infection in the next target cell. While cell-free viral particles released into the extracellular environment are necessary for long distance spread, there are disadvantages to this mechanism. These include the presence of immune system components, the low success rate of infection by single particles, and the relative fragility of viral particles in the environment. Several mechanisms of direct cell-to-cell spread have been reported for animal viruses which would avoid the issues associated with cell-free particles. A number of viruses can utilize several different mechanisms of direct cell-to-cell spread, but our understanding of the differential usage by these pathogens is modest. Although the mechanisms of cell-to-cell spread differ among viruses, there is a common exploitation of key pathways and components of the cellular cytoskeleton. Remarkably, some of the viral mechanisms of cell-to-cell spread are surprisingly similar to those used by bacteria. Here we summarize the current knowledge of the conventional and non-conventional mechanisms of viral spread, the common methods used to detect viral spread, and the impact that these mechanisms can have on viral pathogenesis.

Viruses and viral epidemics in the metabolic theory of evolution

Viruses, including the SARS-CoV-2 virus responsible for the current COVID-19 epidemic, are a key to the understanding of life and evolution. Cells may have arisen from aqueous sequestration inside a lipid envelope studded with chromophores capable of capturing solar photons. Nitrogen incorporation in the primordial cell chemistry allowed synthesis of amino acids and nucleic acids, a prelude to RNA and subsequently DNA. Metagenomics provides access to nucleoprotein sediments synthesised by a googol of metabolically differentiated cells that have marked the evolution of life. Replication of a virus, a nucleoprotein particle, occurs passively in competent cells. Viruses are only identified in the context of the epidemic that they induce as a result of transmission from one host to another. By breaking down the viral particle, the host cell appears to resurrect the metabolic function of the nucleic acid, which synthesises its components without any form of control. Viral products undergo self-assembly and are exported by either exocytosis or cytolysis. In the absence of cells, viruses appear to be inert. However, intracellular contamination of a virus does not always result in replication: the viral genome can disappear, remain latent, wake up, remain embedded in the cellular genome, become an oncogene or induce auto-immunity. The presence of endogenous retroviruses in eukaryotic cells raises the question of their possible role in evolution.

Cytotoxicity and internalization analysis of silicon nanowires in Buffalo Green Monkey cells: a preliminary study to evaluate the possibility of carrying viruses inside the cells

Silicon nanowires (SiNWs) are attractive functional nanomaterials for biomedical applications. The ability to easily tune their size and density, potential biocompatibility, and knowledge of the chemical activation of SiNWs surface make them natural tools to interact with biological materials. We evaluated the possibility of exploiting SiNWs as carriers to introduce organic compounds into cells. The cellular toxicity and the internalization capacity of free-standing and label-free SiNWs were tested on Buffalo Green Monkey cells (BGM). Confocal fluorescent observation of SiNWs conjugated with fluorescein-polyethylene imine (PEI) confirmed the internalization of the NWs into the Buffalo Green Monkey Cells (BGM).

Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms

The most widely-used assays for studying viral entry, including infectivity, cofloatation, and cell-cell fusion assays, yield functional information but provide low resolution of individual entry steps. Structural characterization provides high-resolution conformational information, but on its own is unable to address the functional significance of these conformations. Single virion tracking microscopy techniques provide more detail on the intermediate entry steps than infection assays and more functional information than structural methods, bridging the gap between these methods. In addition, single virion approaches also provide dynamic information about the kinetics of entry processes. This chapter reviews single virion tracking techniques and describes how they can be applied to study specific virus entry steps. These techniques provide information complementary to traditional ensemble approaches. Single virion techniques may either probe virion behavior in live cells or in biomimetic platforms. Synthesizing information from ensemble, structural, and single virion techniques ultimately yields a more complete understanding of the viral entry process than can be achieved by any single method alone.

A two-step heat treatment of cell disruption supernatant enables efficient removal of host cell proteins before chromatographic purification of HBc particles

The thermal stability of HBc particles was systematically investigated for efficient removal of host cell proteins (HCP) by heat treatment before chromatographic step. The HBc particles were found stable up to 80°C for 30 min without any noticeable change in circular dichroism spectra, fluorescence spectra and transmission electron microscope observation. When heating was applied to precipitate the HCP in the cell disruption supernatant of HBc fermentation, the HCP removal effect was more obvious as the temperature went higher. However, a phenomenon was found beyond 70°C where the recovered HBc particles had larger than normal size and molecular weight as observed by dynamic light scattering and multi-angle laser light scattering. Analysis found that the HBc particles possess nanopores which expand with temperature. When the temperature was above 70℃, the pores were large enough for some HCP to penetrate in, but not being able to get out after cooling down. To fully utilize the thermal stability and avoid the interference of HCP entering, a two-step heat treatment strategy was designed. The supernatant was firstly heated up to 60°C for 30 min to precipitate most HCP, then another 30 min at 70°C was used to remove the rest impurities. The two-step heat treatment effectively avoided the HCP entering problem, achieving 85.8% particle recovery and 74.7% purity. With further one-step hydrophobic interaction chromatography, the purity was increased to 99.0% with overall process recovery of 77.7%, considerably higher than those reported in the literature. The same process design was applied to purify three HBc-related products, including OVA-HBc, M2e-HBc and NP-HBc. All recoveries were higher than 50% with purity greater than 97%.

Bifurcation analysis of HIV-1 infection model with cell-to-cell transmission and immune response delay

A within-host viral infection model with both virus-to-cell and cell-to-cell transmissions and time delay in immune response is investigated. Mathematical analysis shows that delay may destabilize the infected steady state and lead to Hopf bifurcation. Moreover, the direction of the Hopf bifurcation and the stability of the periodic solutions are investigated by normal form and center manifold theory. Numerical simulations are done to explore the rich dynamics, including stability switches, Hopf bifurcations, and chaotic oscillations.

Useful Tips, Widely Used Techniques, and Quantifying Cell Metabolic Behavior

The insect cell culture/baculovirus system has three primary applications: (1) recombinant protein synthesis, (2) biopesticide synthesis, and (3) as a model system (e.g., for studying apoptosis). The fundamental techniques involved in these applications are described throughout this book. In this chapter the most widely used techniques are summarized and the reader is directed to detailed information found elsewhere in this book. Furthermore, many useful tips and my personal preferences that are rarely published are discussed in this chapter along with quantitative methods to characterize cell growth, baculovirus infection, and metabolism.

[Ebola virus host cell entry]

Ebola virus is an enveloped virus with filamentous structure and causes a severe hemorrhagic fever in human and nonhuman primates. Host cell entry is the first essential step in the viral life cycle, which has been extensively studied as one of the therapeutic targets. A virus factor of cell entry is a surface glycoprotein (GP), which is an only essential viral protein in the step, as well as the unique particle structure. The virus also interacts with a lot of host factors to successfully enter host cells. Ebola virus at first binds to cell surface proteins and internalizes into cells, followed by trafficking through endosomal vesicles to intracellular acidic compartments. There, host proteases process GPs, which can interact with an intracellular receptor. Then, under an appropriate circumstance, viral and endosomal membranes are fused, which is enhanced by major structural changes of GPs, to complete host cell entry. Recently the basic research of Ebola virus infection mechanism has markedly progressed, largely contributed by identification of host factors and detailed structural analyses of GPs. This article highlights the mechanism of Ebola virus host cell entry, including recent findings.

Globally visualizing the microtubule-dependent transport behaviors of influenza virus in live cells

Understanding the microtubule-dependent behaviors of viruses in live cells is very meaningful for revealing the mechanisms of virus infection and endocytosis. Herein, we used a quantum dots-based single-particle tracking technique to dynamically and globally visualize the microtubule-dependent transport behaviors of influenza virus in live cells. We found that the intersection configuration of microtubules can interfere with the transport behaviors of the virus in live cells, which lead to the changing and long-time pausing of the transport behavior of viruses. Our results revealed that most of the viruses moved along straight microtubules rapidly and unidirectionally from the cell periphery to the microtubule organizing center (MTOC) near the bottom of the cell, and the viruses were confined in the grid of microtubules near the top of the cell and at the MTOC near the bottom of the cell. These results provided deep insights into the influence of entire microtubule geometry on the virus infection.

Super-resolution microscopy: a virus' eye view of the cell

It is difficult to observe the molecular choreography between viruses and host cell components, as they exist on a spatial scale beyond the reach of conventional microscopy. However, novel super-resolution microscopy techniques have cast aside technical limitations to reveal a nanoscale view of virus replication and cell biology. This article provides an introduction to super-resolution imaging; in particular, localisation microscopy, and explores the application of such technologies to the study of viruses and tetraspanins, the topic of this special issue.

HIV trafficking in host cells: motors wanted!

Throughout the viral replication cycle, viral proteins, complexes, and particles need to be transported within host cells. These transport events are dependent on the host cell cytoskeleton and molecular motors. However, the mechanisms by which virus is trafficked along cytoskeleton filaments and how molecular motors are recruited and regulated to guarantee successful integration of the viral genome and production of new viruses has only recently begun to be understood. Recent studies on HIV have identified specific molecular motors involved in the trafficking of these viral particles. Here we review recent literature on the transport of HIV components in the cell, provide evidence for the identity and role of molecular motors in this process, and highlight how these trafficking events may be related to those occurring with other viruses.

Evolutionary dynamics of genome segmentation in multipartite viruses

Multipartite viruses are formed by a variable number of genomic fragments packed in independent viral capsids. This fact poses stringent conditions on their transmission mode, demanding, in particular, a high multiplicity of infection (MOI) for successful propagation. The actual advantages of the multipartite viral strategy are as yet unclear. The origin of multipartite viruses represents an evolutionary puzzle. While classical theories suggested that a faster replication rate or higher replication fidelity would favour shorter segments, recent experimental results seem to point to an increased stability of virions with incomplete genomes as a factor able to compensate for the disadvantage of mandatory complementation. Using as main parameters differential stability as a function of genome length and MOI, we calculate the conditions under which a set of complementary segments of a viral genome would outcompete the non-segmented variant. Further, we examine the likeliness that multipartite viral forms could be the evolutionary outcome of the competition among the defective genomes of different lengths that spontaneously arise under replication of a complete, wild-type genome. We conclude that only multipartite viruses with a small number of segments could be produced in our scenario, and discuss alternative hypotheses for the origin of multipartite viruses with more than four segments.

Interferon-inducible effector mechanisms in cell-autonomous immunity

Interferons (IFNs) induce the expression of hundreds of genes as part of an elaborate antimicrobial programme designed to combat infection in all nucleated cells - a process termed cell-autonomous immunity. As described in this Review, recent genomic and subgenomic analyses have begun to assign functional properties to novel IFN-inducible effector proteins that restrict bacteria, protozoa and viruses in different subcellular compartments and at different stages of the pathogen life cycle. Several newly described host defence factors also participate in canonical oxidative and autophagic pathways by spatially coordinating their activities to enhance microbial killing. Together, these IFN-induced effector networks help to confer vertebrate host resistance to a vast and complex microbial world.

Kinetics of virus production from single cells

The production of virus by infected cells is an essential process for the spread and persistence of viral diseases, the effectiveness of live-viral vaccines, and the manufacture of viruses for diverse applications. Yet despite its importance, methods to precisely measure virus production from cells are lacking. Most methods test infected-cell populations, masking how individual cells behave. Here we measured the kinetics of virus production from single cells. We combined simple steps of liquid-phase infection, serial dilution, centrifugation, and harvesting, without specialized equipment, to track the production of virus particles from BHK cells infected with vesicular stomatitis virus. Remarkably, cell-to-cell differences in latent times to virus release were within a factor of two, while production rates and virus yields spanned over 300-fold, highlighting an extreme diversity in virus production for cells from the same population. These findings have fundamental and technological implications for health and disease.

Protocol for a mammalian cell-based assay for monitoring the HIV-1 protease activity

Proteases are essential at different stages of the viral life cycle and for the establishment of a successful infection. Monitoring the catalytic activity of proteases in an easy and straightforward manner can thus drastically facilitate the discovery of novel antivirals, as well as help elucidate the activity and mechanism of action of the viral protease under study. In our laboratory, we have developed an assay in T-cells with a robust read-out to monitor the proteolytic activity of HIV-1 Protease (PR). The assay utilizes the prototypic transcription factor Gal4, which consists of the N-terminal DNA-binding domain and the C-terminal trans-activation domain. The assay is based upon (1) introduction of PR in between the two Gal4 domains to obtain a PR/Gal4 fusion protein and (2) utilization of the enhanced Green Fluorescent Protein as reporter of PR activity.In order to overcome the possible cellular cytotoxicity of PR, the fusion protein in our assay is under the control of a tetracycline-inducible promoter. This ensures that it will be expressed only when needed, upon the addition of tetracycline or doxycycline. When active, PR has autocatalytic activity and cleaves itself from the Gal4 domains, resulting in the inability to induce eGFP expression. However, if PR activity is blocked or it is inactive, the two domains remain intact, resulting in eGFP expression. The assay can therefore be utilized to analyze the inhibitory effects of factors, peptides or compounds, designed on a rational- or nonrational-based approach, in the natural milieu of infection, where eGFP serves as a biosensor for PR activity.

Imaging multiple intermediates of single-virus membrane fusion mediated by distinct fusion proteins

Membrane fusion plays an essential role in the entry of enveloped viruses into target cells. The merging of viral and target cell membranes is catalyzed by viral fusion proteins, which involves multiple sequential steps in the fusion process. However, the fusion mechanisms mediated by different fusion proteins involve multiple transient intermediates that have not been well characterized. Here, we report a synthetic virus platform that allows us to better understand the different fusion mechanisms driven by the diverse types fusion proteins. The platform consists of lentiviral particles coenveloped with a surface antibody, which serves as the binding protein, along with a fusion protein derived from either influenza virus (HAmu) or Sindbis virus (SINmu). By using a single virus tracking technique, we demonstrated that both HAmu- and SINmu-bearing viruses enter cells through clathrin-dependent endocytosis, but they required different endosomal trafficking routes to initiate viral fusion. Direct observation of single viral fusion events clearly showed that hemifusion mediated by SINmu upon exposure to low pH occurs faster than that mediated by HAmu. Monitoring sequential fusion processes by dual labeling the outer and inner leaflets of viral membranes also revealed that the SINmu-mediated hemifusion intermediate is relatively long-lived as compared with that mediated by HAmu. Taken together, we have demonstrated that the combination of this versatile viral platform with the techniques of single virus tracking can be a powerful tool for revealing molecular details of fusion mediated by various fusion proteins.

Computational fitness landscape for all gene-order permutations of an RNA virus

How does the growth of a virus depend on the linear arrangement of genes in its genome? Answering this question may enhance our basic understanding of virus evolution and advance applications of viruses as live attenuated vaccines, gene-therapy vectors, or anti-tumor therapeutics. We used a mathematical model for vesicular stomatitis virus (VSV), a prototype RNA virus that encodes five genes (N-P-M-G-L), to simulate the intracellular growth of all 120 possible gene-order variants. Simulated yields of virus infection varied by 6,000-fold and were found to be most sensitive to gene-order permutations that increased levels of the L gene transcript or reduced levels of the N gene transcript, the lowest and highest expressed genes of the wild-type virus, respectively. Effects of gene order on virus growth also depended upon the host-cell environment, reflecting different resources for protein synthesis and different cell susceptibilities to infection. Moreover, by computationally deleting intergenic attenuations, which define a key mechanism of transcriptional regulation in VSV, the variation in growth associated with the 120 gene-order variants was drastically narrowed from 6,000- to 20-fold, and many variants produced higher progeny yields than wild-type. These results suggest that regulation by intergenic attenuation preceded or co-evolved with the fixation of the wild type gene order in the evolution of VSV. In summary, our models have begun to reveal how gene functions, gene regulation, and genomic organization of viruses interact with their host environments to define processes of viral growth and evolution.

Although many viruses are linked to diseases that adversely impact the health of their human, animal, and plant hosts, viruses could help promote wellness and treat disease if their “good traits” could be harnessed. Potentially useful virus traits include their abilities to stimulate a robust immune response, target specific tissues for the delivery of foreign genes, and destroy tumors. The exploitation of such traits in the engineering of virus-based vaccines, gene therapies and anti-cancer strategies is limited in part by our inability to control how viruses grow. Generally, viruses that grow poorly will be more desirable for vaccine applications, whereas viruses that grow and spread rapidly will be useful for destroying tumors. Further, gene therapies will rely on controlling the extent to which a therapeutic gene is delivered and expressed. Robust methods for controlling virus growth have yet to be discovered. However, for some viruses, such as vesicular stomatitis virus (VSV), growth can be very sensitive to the specific linear order of its five genes. Our current work is significant in combining experiments and computational models to identify which virus genes and genome positions most sensitively impact VSV growth, providing a foundation for its applications in human health.

[Vaccines, biotechnology and their connection with induced abortion]

Diploid cells (WI-38, MRC-5) vaccines have their origin in induced abortions. Among these vaccines we fi nd the following: rubella, measles, mumps, rabies, polio, smallpox, hepatitis A, chickenpox, and herpes zoster. Nowadays, other abortion tainted vaccines cultivated on transformed cells (293, PER.C6) are in the pipeline: flu, Respiratory Syncytial and parainfluenza viruses, HIV, West Nile virus, Ebola, Marburg and Lassa, hepatitis B and C, foot and mouth disease, Japanese encephalitis, dengue, tuberculosis, anthrax, plague, tetanus and malaria. The same method is used for the production of monoclonal antibodies and other proteins, gene therapy and genomics. Technology enables us to develop the aforementioned products without resorting to induced abortion. Full disclosure of the cell origin in the labelling of vaccines and other products must be supported. There are vaccines from non-objectionable sources which should be made available to the public. When no alternative vaccines exist, ethical research must be promoted. Non-objectionable sources in the production of monoclonal antibodies, gene therapy and genomics must be encouraged. It is not be consistent to abstain from products originated in embryonic stem cells and at the same time approve of products obtained from induced abortions. It is of paramount importance to avoid that induced abortion technology seeps into every field of Medicine.

Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells

Viruses can reproduce their progenies only within a host cell, and their actions depend both on its destructive tendencies toward a specific host cell and on environmental conditions. Therefore, knowledge of the subcellular localization of viral proteins in a host cell or virus-infected cell is very useful for in-depth studying of their functions and mechanisms as well as designing antiviral drugs. An analysis on the Swiss-Prot database (version 50.0, released on May 30, 2006) indicates that only 23.5% of viral protein entries are annotated for their subcellular locations in this regard. As for the gene ontology database, the corresponding percentage is 23.8%. Such a gap calls for the development of high throughput tools for timely annotating the localization of viral proteins within host and virus-infected cells. In this article, a predictor called "Virus-PLoc" has been developed that is featured by fusing many basic classifiers with each engineered according to the K-nearest neighbor rule. The overall jackknife success rate obtained by Virus-PLoc in identifying the subcellular compartments of viral proteins was 80% for a benchmark dataset in which none of proteins has more than 25% sequence identity to any other in a same location site. Virus-PLoc will be freely available as a web-server at http://202.120.37.186/bioinf/virus for the public usage. Furthermore, Virus-PLoc has been used to provide large-scale predictions of all viral protein entries in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The results thus obtained have been deposited in a downloadable file prepared with Microsoft Excel and named "Tab_Virus-PLoc.xls." This file is available at the same website and will be updated twice a year to include the new entries of viral proteins and reflect the continuous development of Virus-PLoc.

A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells

Biological trajectories can be characterized by transient patterns that may provide insight into the interactions of the moving object with its immediate environment. The accurate and automated identification of trajectory motifs is important for the understanding of the underlying mechanisms. In this work, we develop a novel trajectory segmentation algorithm based on supervised support vector classification. The algorithm is validated on synthetic data and applied to the identification of trajectory fingerprints of fluorescently tagged human adenovirus particles in live cells. In virus trajectories on the cell surface, periods of confined motion, slow drift, and fast drift are efficiently detected. Additionally, directed motion is found for viruses in the cytoplasm. The algorithm enables the linking of microscopic observations to molecular phenomena that are critical in many biological processes, including infectious pathogen entry and signal transduction.

Host factors exploited by retroviruses

Retroviruses make a long and complex journey from outside the cell to the nucleus in the early stages of infection, and then an equally long journey back out again in the late stages of infection. Ongoing efforts are identifying an enormous array of cellular proteins that are used by the viruses in the course of their travels. These host factors are potential new targets for therapeutic intervention.

Avian reovirus: Structure and biology

Avian reoviruses are important pathogens that cause considerable losses to the poultry industry, but they have been poorly characterized at the molecular level in the past, mostly because they have been considered to be very similar to the well-studied mammalian reoviruses. Studies performed over the last 20 years have revealed that avian reoviruses have unique properties and activities, different to those displayed by their mammalian counterparts, and of considerable interest to molecular virologists. Notably, the avian reovirus S1 gene is unique, in that it is a functional tricistronic gene that possesses three out-of-phase and partially overlapping open reading frames; the identification of the mechanisms that govern the initiation of translation of the three S1 cistrons, and the study of the properties and activities displayed by their encoded proteins, are particularly interesting areas of research. For instance, avian reoviruses are one of the few nonenveloped viruses that cause cell-cell fusion, and their fusogenic phenotype has been associated with a nonstructural 10 kDa transmembrane protein, which is expressed by the second cistron of the S1 gene; the small size of this atypical fusion protein offers an interesting model for studying the mechanisms of cell-cell fusion and for identifying fusogenic domains. Finally, avian reoviruses are highly resistant to interferon, and therefore they may be useful for investigating the mechanisms and strategies that viruses utilize to counteract the antiviral actions of interferons.

Polymer-templated microarrays for highly reliable plaque purification

To infect cells with a particular multiplicity of infection, it is essential to know the concentration of virus in the inoculum. Here we describe a highly reliable and controllable method for plaque purification using cell-repellent surfaces micropatterned on the substrate. Micropatterning of localized chemical or biochemical domains has the potential to become a powerful tool in controlling the seeding of cells. The cell array was reliably fabricated with micropatterned surfaces, and the number of cells in a pattern was easily controlled by the cell density in the media and micropattern size. The cell micropatterns were infected with baculoviruses to form an array of virus plaques. GFP-modified and wild-type baculoviruses were used to verify the feasibility of purifying a specific plaque. Using confocal microscopy, GFP-expressing plaques were readily selectable and removable.

[How the poliovirus changes a cell]

The paper considers different aspects of a cell response to poliovirus infection, such as transcriptional and translational changes, modification of membranes and their transport, impairment in the nucleoplasmic barrier, and the mechanisms of infected cell death.

Nucleopolyhedrovirus infected central nervous system cells of Bombyx mori (L.) (Lepidoptera: Bombycidae)

BmMNPV, a Nucleopolyhedrovirus isolated from infected Bombyx mori (L.) larvae in Paraná State--Brazil, was used to inoculate healthy 5th-instar B. mori larvae and examine the infection on central nervous system (CNS) cells. Samples of nervous tissue were removed from the infected insects, at different sampling times, and processed for cytopathology studies by light and transmission electron microscopy using routine techniques. The experiment included both inoculated and non-inoculated larvae (control). BmMNPV infection was detected on the 5th day after inoculation in CNS cells. Initially, infection was characterized by nuclear hypertrophy and the presence of virogenic stroma, in which the progeny virions were produced. Virions are enveloped and occluded into protein crystal, the polyhedra. Lyses of infected CNS cells were undetected; however, free mature polyhedra were seen in spaces inside the CNS. These polyhedra possibly came from trachea that penetrate the CNS and its cells, which are susceptible to BmMNPV and lyses after infection. We conclude that the tracheal system is responsible for disseminating BmMNPV infection in B. mori CNS and that the tracheal branches allow non-occluded virions to pass through the blood-brain barrier.

Cellular factors influencing Semliki Forest Virus vector biology

Viral vectors are currently the best tools for gene delivery in a therapeutic setting, especially for in vivo use. Alphaviruses, a family of positive singlestranded RNA viruses, have been engineered to allow the formation of a highly efficient replicon. Using these replicons, it is possible to generate recombinant particles. Parental viruses and recombinant vectors share certain pathways while interacting with their target cells. In this review, we describe the consecutive events leading to transduction, and transgene expression, in view of the cellular factors that affect each individual step. Classical virology will benefit from the knowledge accumulated studying vectors, and such work will shed light on crosstalk between intruding viruses and their hosts. Ultimately, these data should help the design of vectors adapted to specific target cells.

Reengineering transfusion and cellular therapy processes hospitalwide: ensuring the safe utilization of blood products

Efforts to make blood transfusion as safe as possible have focused on making the blood in the bag as disease-free as possible. The results have been dramatic, and the costs have been correspondingly high. Although blood services will have to continue to deal with emerging pathogens, efforts to reduce the transfusion of infectious agents presently posing a risk will require high incremental costs and result in only improvements of a small magnitude. The other aspect of safe blood transfusion, the actual transfusion process performed primarily in hospitals, has been accorded considerably less interest. We should turn our attention to enhancing overall blood safety by focusing on improving the process of blood transfusion. Errors involving patient, specimen, and blood product identification put transfused patients at risk, increasing the mortality risk for some. Solutions that could improve the transfusion process are discussed as a focus of this article.

HIV dynamics with multiple infections of target cells

The high incidence of multiple infections of cells by HIV sets the stage for rapid HIV evolution by means of recombination. Yet how HIV dynamics proceeds with multiple infections remains poorly understood. Here, we present a mathematical model that describes the dynamics of viral, target cell, and multiply infected cell subpopulations during HIV infection. Model calculations reproduce several experimental observations and provide key insights into the influence of multiple infections on HIV dynamics. We find that the experimentally observed scaling law, that the number of cells coinfected with two distinctly labeled viruses is proportional to the square of the total number of infected cells, can be generalized so that the number of triply infected cells is proportional to the cube of the number of infected cells, etc. Despite the expectation from Poisson statistics, we find that this scaling relationship only holds under certain conditions, which we predict. We also find that multiple infections do not influence viral dynamics when the rate of viral production from infected cells is independent of the number of times the cells are infected, a regime expected when viral production is limited by cellular rather than viral factors. This result may explain why extant models, which ignore multiple infections, successfully describe viral dynamics in HIV patients. Inhibiting CD4 down-modulation increases the average number of infections per cell. Consequently, altering CD4 down-modulation may allow for an experimental determination of whether viral or cellular factors limit viral production.

Diverse apoptotic pathways in enterovirus 71-infected cells

Mechanisms related to the neuropathogenesis of enterovirus 71 infection remain unclear. This investigation conducts a comprehensive study of the apoptotic pathways in neural and non-neural cells following enterovirus 71 infection. Infections with enterovirus 71 not only induce classical cytopathic effects in SF268 (human glioblastoma), SK-N-MC (human neuroblastoma), RD, and Vero cells, but also induce classic signs of apoptosis in all cells, including DNA fragmentation and phosphatidylserine translocation. Apoptosis has also been caused by the efflux of cytochrome c from mitochondria, and subsequently by cleavage of caspase 9 in all cells. Activation of caspase 8 followed by cleavage of the proapoptotic protein Bid only occurs in non-neural cells. Results of this study demonstrate that a mitochondrial pathway of apoptosis mediated by activation and cleavage of caspase 9 is a main pathway in enterovirus 71-induced apoptosis, especially for enterovirus 71-infected neural cells.

A novel method for detection of virus-infected cells through moving optical gradient fields using adenovirus as a model system

BACKGROUND

Most methods for cellular analysis require labeling with specific antibodies or dyes and are often destructive. We have developed a technology called Optophoresis trade mark, which measures cell physiology based on the cell's motion in a near-infrared optical gradient. This technique does not require labels, is nondestructive, and involves minimal sample processing.

METHODS

We have used Optophoresis to interrogate nonproductive and productive adenovirus-infected cell lines. Using an adenoviral vector containing green fluorescent protein (GFP) as a secondary assay, we show that viral infection can be monitored with Optophoresis.

RESULTS

In HeLa cells, adenovirus infection after 24 h caused a 12% to 17% increase in optophoretic motility of the cells. In 293 cells, adenovirus infection resulted in a 40% increase in the optophoretic motility. The P values obtained were 4.5 x 10(-11) between noninfected and infected HeLa cells, and 2.1 x 10(-13) between noninfected and infected 293 cells. Cells infected with adenovirus lacking the GFP reporter gene gave similar shifts. In a time course, we observed an optophoretic shift after 4 h of infection, well before GFP expression.

CONCLUSIONS

Optophoresis provides nondestructive, label-free analysis of viral infection. Detection is independent of reporter gene expression and can be observed early in the infection process.

A Protein Sequestering System Reveals Control of Cellular Programs by the Transcriptional Coactivator HCF-1

The mammalian transcriptional coactivator HCF-1 is a critical component of the multiprotein herpes simplex virus immediate early gene enhancer core complex. The protein has also been implicated in basic cellular processes such as cell-cycle progression, transcriptional coactivation, and mRNA processing. Functions have been attributed to HCF-1 primarily from analyses of protein-protein interactions and from the cell-cycle-arrested phenotype of an HCF-1 temperature-sensitive mutant. However, neither the mechanisms involved nor specific cellular transcriptional targets have been identified. As the protein is essential for cell viability and proliferation, a genetic system was developed to specifically sequester the nuclear factor in the cell cytoplasm in a regulated manner. This approach exhibits no significant cell toxicity yet clearly demonstrates the requirement of available nuclear HCF-1 for herpes simplex virus immediate early gene expression during productive infection. Additionally, cellular transcriptional events were identified that contribute to understanding the functions ascribed to the protein and implicate the protein in events that impact the regulation of critical cellular processes.

TRAIL and viral infection

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the TNF family that can induce apoptosis when binding to either of two receptors bearing an intracellular death domain. The physiologic function of the TRAIL system, which also comprises three receptors not mediating a death signal has just begun to be elucidated. Expression of TRAIL, mostly upon stimulation by interferons, in different cytotoxic immune cells suggested it has a role as an important effector molecule in immune surveillance. In addition to its ability to induce apoptosis in transformed tumor cells, TRAIL has attracted attention for its possibly critical role in the defense against viral infection. Viruses may induce TRAIL expression in host and?or immune cells and sensitize host cells toward TRAIL-mediated apoptosis. On the other hand, viruses have evolved a variety of strategies to prevent TRAIL-mediated host cell death early in infection, which may contribute to allowing their replication and the spread of viral progeny. The knowledge of the molecular mechanisms leading to modification of TRAIL sensitivity in virus-host cell interactions may also impact upon future (virus-based) strategies to increase TRAIL sensitivity of tumor cells.

Optimizing within-host viral fitness: infected cell lifespan and virion production rate

We explore how an infected cell's virion production rate can affect the relative fitness of a virus within a host. We perform an invasion analysis, based on an age-structured model of viral dynamics, to derive the within-host relative viral fitness. We find that for chronic infections, in the absence of trade-offs between viral life history stages, natural selection favors viral strains whose virion production rate maximizes viral burst size. We then show how various life history trade-offs such as that between virion production and immune system recognition and clearance of virally infected cells can lead to natural selection favoring production rates lower than the one that maximizes burst size. Our findings suggest that HIV replication rates should vary between cells with different life spans, as has been suggested by recent observation.

How viruses enter animal cells

Viruses replicate within living cells and use the cellular machinery for the synthesis of their genome and other components. To gain access, they have evolved a variety of elegant mechanisms to deliver their genes and accessory proteins into the host cell. Many animal viruses take advantage of endocytic pathways and rely on the cell to guide them through a complex entry and uncoating program. In the dialogue between the cell and the intruder, the cell provides critical cues that allow the virus to undergo molecular transformations that lead to successful internalization, intra-cellular transport, and uncoating.

Targeting TFIIH to inhibit host cell transcription by Rift Valley Fever Virus

In the February 20 issue of Cell, report that Rift Valley Fever Virus (RVFV) targets cellular transcriptional apparatus to inhibit RNA polymerase II-mediated transcription. Unlike polio and vesicular stomatitis viruses, both of which target the TATA binding protein (TBP), RVFV appears to target the basal transcription factor THIIH to induce shut-off of host cell transcription.

The story of cell fusion: big lessons from little worms

The ability of two or more cells to unite to form a new syncytial cell has been utilized in metazoans throughout evolution to form many complex organs, such as muscles, bones and placentae. This requires migration, recognition and adhesion between cells together with fusion of their plasma membranes and rearrangement of their cytoplasmic contents. Until recently, understanding of the mechanisms of cell fusion was restricted to fusion between enveloped viruses and their target cells. The identification of new factors that take part in developmental cell fusion in C. elegans opens the way to understanding how cells fuse and what the functions of this process are. In this review, we describe current knowledge on the mechanisms and putative roles of developmental cell fusion in C. elegans and how cell fusion is regulated, together with other intercellular processes to promote organogenesis.

Interaction of hepatitis B virus with cells

Virus infection is initiated by recognition and attachment of the virus to the cell surface. Despite the fact that this interaction determines the virus-related pathogenesis, its molecular basis remained obscure for HBV. This process is mediated primarily by the viral envelope and the cellular receptors. HBV infection is not exceptional in this regard but its putative receptors have not been identified yet. The recent development of protocols to establish HBV susceptible cell lines and unique tools to measure HBV-cell attachment at a single cell resolution set the stage for the study of HBV-host cell interaction. These studies revealed that the QLDPAF epitope of the HBV surface antigen large protein (LHBsAg) plays a major role in this process. Quantitative measurements suggested the presence of a second player in this process and both act synergistically to improve cell attachment. As the step of virus-cell attachment is potentially susceptible to specific inhibitors, understanding the molecular basis of virus-cell attachment can be expected to have therapeutic impacts.

Charting HIV's remarkable voyage through the cell: Basic science as a passport to future therapy

Adequate control of HIV requires impairing the infection, replication and spread of the virus, no small task given the extraordinary capacity of HIV to exploit the cell's molecular machinery in the course of infection. Understanding the dynamic interplay of host cell and virus is essential to the effort to eradicate HIV.

Viruses and interferons

The interferon system is the first line of defense against viral infection in mammals. This system is designed to block the spread of virus infection in the body, sometimes at the expense of accelerating the death of the infected cells. As expected of potent cytokines, in addition to their antiviral effects, interferons have profound effects on many aspects of cell physiology. All these actions of interferons are mediated by hundreds of interferon-induced proteins that are usually not synthesized in resting cells. Interferons induce their synthesis by activating the Jak-STAT pathways, a paradigm of cell signaling used by many cytokines and growth factors. Surprisingly, some of the same genes can also be induced directly by viruses and double-stranded RNA, a common viral by-product. Some of the interferon-induced proteins have novel biochemical properties and some are inactive as such but can be activated by double-stranded RNA produced during virus infection. Finally, almost all viruses have evolved mechanisms to evade the interferon system by partially blocking interferon synthesis or interferon action. Thus, in nature interferons and viruses maintain an equilibrium that allows regulated viral replication.

Determinants for lentiviral infection of non-dividing cells

Lentiviruses share the common characteristic of infecting non-dividing target cells, distinguishing them from the oncogenic retroviruses which only productively infect dividing cells. The search for determinants for infection of non-dividing cells has produced a number of candidates. From HIV-1, the viral proteins matrix, integrase and Vpr have all been implicated. A structural determinant, the central DNA flap, has also been implicated. The supporting evidence for each of these proposed determinants will be examined and compared to how other viruses, non-retroviruses, transport their genomes to the nucleus. With currently available data, integrase and the central DNA flap appear to be the key players, and yet the mechanism for infection of non-dividing cells remains undefined.

Virus-cell interactions: impact on cytokine production, immune evasion and tumor growth

The outcome of a viral infection ranges from benign to fatal with the clinical pictures being very diverse. This is largely due to the virus-cell interactions that occur in the infected organism. Rapidly after infection, cells initiate a first line of defense against the virus. The cells sense viruses through several mechanisms. Among these the ability to respond to accumulation of double-stranded RNA has been particularly well studied and seems to be of importance. On the other hand, the close co-existence of virus and host has allowed viruses to develop mechanisms to down-modulate the initial reaction or to exploit this proinflammatory response in its own advance. This review describes how virus infections affect cellular signal transduction and the mechanisms through which certain viruses modulate this response to dampen the immune response or prevent cell death.