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Papillomavirus (PV) is a well-known pathogen associated with epithelial and mucosal neoplastic diseases. In contrast to human PVs, characterization of animal PVs from the aspect of anogenital neoplasm is still on a learning curve. In the present study, two vulval and one anal warts, histologically diagnosed as fibropapillomas, excised from dairy cattle were analyzed. PCR and sequencing revealed that bovine papillomavirus type 1 (BPV-1) and BPV-2 were detected from anal and vulval fibropapillomas, respectively. Immunohistochemistry detected PV antigen in a few differentiated keratinocytes of one vulval case. Reverse-transcriptase PCR detected the early region, but not the late region of BPV mRNA in all three cases. The present study will provide new insight into the relationship between BPV and anogenital papilloma in cattle.

Direct interaction between intrinsically disordered proteins (IDPs) is often difficult to characterize hampering the elucidation of their binding mechanism. Particularly challenging is the study of fuzzy complexes, in which the intrinsically disordered proteins or regions retain conformational freedom within the assembly. To date, nuclear magnetic resonance spectroscopy has proven to be one of the most powerful techniques to characterize at the atomic level intrinsically disordered proteins and their interactions, including those cases where the formed complexes are highly dynamic. Here, we present the characterization of the interaction between a viral protein, the Early region 1A protein from Adenovirus (E1A), and a disordered region of the human CREB-binding protein, namely the fourth intrinsically disordered linker CBP-ID4. E1A was widely studied as a prototypical viral oncogene. Its interaction with two folded domains of CBP was mapped, providing hints for understanding some functional aspects of the interaction with this transcriptional coactivator. However, the role of the flexible linker connecting these two globular domains of CBP in this interaction was never explored before.

Extensive studies on viral-mediated oncogenic transformation by human adenoviruses have revealed much of our current understanding on the molecular mechanisms that are involved in the process. To date, these studies have shown that cell transformation is a multistep process regulated by the cooperation of several adenoviral gene products encoded in the early regions 1 (E1) and 4 (E4). Early region 1A immortalizes primary rodent cells, whereas co-expression of early region protein 1B induces full manifestation of the transformed phenotype. Beside E1 proteins, also some E4 proteins have partial transforming activities through regulating many cellular pathways. Here, we summarize recent data of how adenoviral oncoproteins may contribute to viral transformation and discuss the challenge of pinpointing the underlying mechanisms.

The allosteric property of globular proteins is applauded as their intrinsic ability to regulate distant sites, and this property further plays a critical role in a wide variety of cellular regulatory mechanisms. Recent advancements and studies have revealed the manifestation of allostery in intrinsically disordered proteins or regions as allosteric sites present within or mediated by IDP/IDRs facilitates the signaling interactions for various biological mechanisms which would otherwise be impossible for globular proteins to regulate. This thematic review has highlighted the biological outcomes that can be achieved by the mechanism of allosteric regulation of intrinsically disordered proteins or regions. The similar mechanism has been implemented on Adenovirus 5 early region 1A and tumor apoptosis protein p53 in correspondence with other partners in binary and ternary complexes, which are the subject of the current review. Both these proteins regulate once they bind to their partners, consequently, forming either a binary or a ternary complex. Allosteric regulation by IDPs is currently a subject undergoing intense study, and the ongoing research work will ensure a better understanding of precision and efficiency of cellular regulation by them. Allosteric regulation mechanism can also be researched by intrinsically disordered protein-specific force field.

BackgroundHIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant.MethodsWe analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters.ResultsOur meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1-7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990-1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years.ConclusionThese data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.

The small-DNA human adenovirus encodes one of the most versatile molecular hubs, the E1A protein. This protein is essential for productive viral infection in human cells and a vast amount of biologically relevant data are available on its interactions with host proteins. Up to now, however, no high-resolution structural and dynamic information on E1A is available despite its important biological role. Among the different spliced variants of E1A, two are expressed at high level in the early stage of infection. These are 243 and 289 residues isoforms. Herein, we present their NMR characterization, showing that they are both highly disordered, but also demonstrate a certain heterogeneous behavior in terms of structural and dynamic properties. Furthermore, we present the characterization of the isolated domain of the longer variant, known as CR3. This study opens the way to understanding at the molecular level how E1A functions.

The present study examines the configuration of an offset jet issuing into a narrow and deep pool. The standard k-&epsilon, model with volume-of-fluid (VOF) method was used to simulate the offset jet for three exit offset ratios (OR = 1, 2 and 3), three expansion ratios (ER = 3, 4 and 4.8), and different jet exits (circular and rectangular). The results clearly show significant effects of the circumference of jet exits (Lexit) in the early region of flow development, and a fitted formula is presented to estimate the length of the potential core zone (LPC). Analysis of the flow field for OR = 1 showed that the decay of cross-sectional streamwise maximum mean velocity (Um) in the transition zone could be fitted by power law with the decay rate n decreased from 1.768 to 1.197 as the ER increased, while the decay of Um for OR = 2 or 3 was observed accurately estimated by linear fit. Analysis of the flow field of circular offset jet showed that Um for OR = 2 decayed fastest due to the fact that the main flow could be spread evenly in floor-normal direction. For circular jets, the offset ratio and expansion ratio do not affect the spread of streamwise velocity in the early region of flow development. It was also observed that the absence of sudden expansion of offset jet is analogous to that of a plane offset jet, and the flow pattern is different.

Polyomaviruses have so far only been isolated from mammals and birds. Typical for all members of this family is their double-stranded genome of approximately 5000 base-pairs which can be divided into an early region encoding at least two functional proteins, the large and small tumor antigens, and a late region encompassing genes for the capsid proteins VP1 and VP2. During the last 10 years several novel polyomaviruses have been described in non-human primates and man. This review compares the non-human primate polyomavirus genomes that have been completely sequenced with each other and with the genomes of human polyomaviruses. We predict the presence of protein- and microRNA-encoding sequences. Our analyses demonstrate that several genetically distinct groups of non-human primate polyomaviruses exist, that different polyomaviruses can infect the same non-human primate species but that most of their proteins display highly similar domains and motifs, indicating conservation of key functions.

The pattern of organization of RNA polymerase II (RNAPII) in wild-type and mutant cs1085 SV40 chromosomes isolated between 30 min and 48 h post-infection was determined using a combination of chromatin immunoprecipitation (ChIP) techniques. During the course of a wild-type infection, we observed a slow but significant decline in the relative occupancy of RNAPII at the early region and a corresponding increase in occupation in the late region. In the promoter, occupancy began high, decreased to a minimum at 8 h post-infection, and then increased to a high level by 48 h post-infection. In the mutant cs1085, which does not down-regulate early transcription, we observed high occupancy of the early region and the promoter throughout the infection. The changing organization of RNAPII on the wild-type SV40 but not the mutant cs1085 genome appears to be a result of the switch from early to late transcription.

This manuscript will contain a brief review of adenovirus (Ad) biology including its structure and the spectrum of clinical diseases that it causes. Newer findings about the interactions of Ad early region 3 (E3) proteins with host proteins and signal transduction processes, which control the inflammatory response, will be described. Some of these processes affect the strategies for using Ads as vectors for gene therapy. There are many excellent reviews of some of these aspects 1. The history of the discoveries that led to the use of Ads as vectors as well as key experiments that resulted in improvements to various aspects of these systems have also been reviewed recently 2. The use of Ad E3 immunoregulatory genes to facilitate allogeneic transplantation and prevent autoimmune diabetes will be described.

C3H 10T1/2 fibroblasts are converted to fully transformed phenotype following coexpression of an activated c-Ha-ras gene and either a constitutively expressed viral or cellular myc gene. In this report, we examined whether the early region 1A (E1A) of adenovirus 5, which synergizes with ras to convert primary embryonic cells to a transformed phenotype, can synergize with ras to transform the established mouse embryonic cell line, C3H 10T1/2. We demonstrate that coexpression of ras and E1A generated a transformed phenotype that could be scored by colony assays and by soft agarose assays but not by standard focus assays. The ras-E1A-transformed phenotype relies on sequences present in conserved regions 1 and 2 of the E1A proteins and, in part, on information encoded by the extreme carboxy terminus of E1A. The contrast between the transformed phenotypes generated following the transfection of C3H 10T1/2 cells with either ras and myc or ras and E1A suggests that myc and E1A cooperate with ras to transform C3H 10T1/2 cells by mechanisms that can be distinguished using this established cell line as a model system.

Adenovirus early region 4 (E4) regulates processes in infected cells that include viral late gene expression, nonhomologous end joining, responses to DNA damage, and apoptosis. E4 is essential for viral growth in most cell lines. In this chapter, the current knowledge of the functions of six E4 products is summarized briefly. Protocols are presented for manipulation of E4, incorporation of E4 mutations into the viral genome, and growth of E4 mutants on complementing cell lines. A compilation of the described E4-complementing cell lines is included.

We present many algorithmic improvements in our early region filling technique, which in a previous publication was already proved to be correct for all connected digital pictures. Ours is an integer-only method that also finds all interior points of any given digital picture by displaying and storing them in a locating matrix. Our filling/locating program is applicable both in computer graphics and image processing.

Adenovirus early region 1A (AdE1A) binds to the C-terminal binding protein 1 (CtBP1) primarily through a highly conserved PXDLS motif located close to its C-terminus. Purified synthetic peptides equivalent to this region of AdE1A have been shown to form a series of {beta}-turns. In this present study the effect of CtBP1 binding on the conformation of C-terminal region of Ad12E1A has been investigated. Using one- and two-dimensional {sup 1}H NMR spectroscopy, the conformation of 20-residue peptides equivalent to amino acids I{sup 241}-V{sup 260} and E{sup 247}-N{sup 266} of Ad12E1A were examined in the absence of CtBP1. Whilst the latter peptide forms a series of {beta}-turns in its C-terminal half as reported previously, the former peptide is {alpha}-helical over the region D{sup 243}-Q{sup 253}. Upon interaction with CtBP1 the conformation of the backbone in the region {sup 255}PVDLCVK{sup 261} of the Ad12E1A E{sup 247}-N{sup 266} peptide reorganises from a predominately {beta}-turn to an {alpha}-helical conformation. This structural isomerisation is characterised by a shift upfield of 0.318 ppm for the {delta}-CH{sub 3} proton resonance of V{sup 256}. 2-D NOESY experiments showed new signals in the amide-{alpha} region which correlate to transferred NOEs from the protein to the peptide residues E{sup 251}, V{supmore » 256} and K{sup 261}. In further analyses the contribution of individual amino acids within the sequence {sup 254}VPVDLS{sup 259} was assessed for their importance in determining structure and consequently affinity of the peptide for CtBP. It has been concluded that Ad12E1A residues {sup 255}P-V{sup 260} serve initially as a recognition site for CtBP and then as an anchor through a {beta}-turns {sup {yields}} {alpha}-helix conformational rearrangement. In addition it has been predicted that regions N-terminal to the PXDLS motif in AdE1As from different virus serotypes and from mammalian proteins form {alpha}-helices.« less

The late region of the three primate polyomaviruses (JCV, BKV, and SV40) encodes a small, highly basic protein known as agnoprotein. While much attention during the last two decades has focused on the transforming proteins encoded by the early region (small and large T-antigens), it has become increasingly evident that agnoprotein has a critical role in the regulation of viral gene expression and replication, and in the modulation of certain important host cell functions including cell cycle progression and DNA repair. The importance of agnoprotein is underscored by its expression during lytic infection of glial cells by JCV that occurs in progressive multifocal leukoencephalopathy (PML), and also in some JCV-associated human neural tumors particularly medulloblastoma. In this review, we will discuss the structure and function of agnoprotein in the viral life cycle during the course of lytic infection and the consequences of agnoprotein expression for the host cell. © 2004 Wiley-Liss, Inc.

Background: In the USA, a high prevalence rate of cytomegalovirus (CMV) excretion among children in day-care centres was reported. However, there is no research about the prevalence rate of CMV among children in day-care centres in Japan. Methods: The CMV excretion was studied in 54 children’s saliva samples, collected from two different day-care centres in Tokyo. As a control, the prevalence of CMV was studied among 61 healthy children who did not attend any day-care centers. The CMV DNA in saliva were examined by polymerase chain reaction (PCR) analysis with one pair of primers for the immediate early region. The sequence of CMV genomes were examined in CMV PCR positive samples. Results: Of the 54 saliva samples, 20.6% (6/29) and 24% (6/25) were CMV PCR positive in children at A and B day-care centres, respectively. The overall positivity of CMV PCR in saliva was 22.2% (12/54). Of the 61 saliva samples as the control study, 6.5% (4/61) were CMV PCR positive. There was a difference in the positivity in each age group of day-care centres and normal control. Each sample of the same day-care center gave conclusive and identical sequence results. Conclusion: We suspected that in each day-care center that there was one prevailing viral strain. We suppose that CMV infections were acquired inside the day-care centres. This is a first report which described viral transmission in day-care centres in Japan.

Publisher Summary This chapter discusses the recent advances in the understanding of the relationship between the adenovirus E1 proteins and the cellular components with which they interact. Hopefully this will shed new light on the means by which adenoviral E1 proteins affect target cells both during transformation and infection. It provides pointers to general mechanisms of cell transformation and oncogenesis. Adenovirus early region 1 encodes four major proteins—two from E1A and two from E1B. Ad E1A is the first protein to be expressed during viral infection and is essential for Ad-mediated transformation. Ad E1A is expressed at high levels only in an insoluble form requiring denaturation for solubilization, Ad E1A is difficult to crystallize and the limited evidence available suggests that the structure of the protein may be appreciably dependent on binding partners. The Ad E1B gene encodes two major proteins. Adenoviruses have assumed a new significance as therapeutic tools. While many of the organisms used for gene delivery have deletions in the E1 region, two other mutant adenoviruses that have potential in the search for antitumor agents are ONYX-015 virus and mini E1A.

Abstract Nonuniform perforation properties and permeability variations close to the wellbore introduce heterogeneities which affect the injectivity decline in water injection wells. We present a method to calculate these effects and derive results for a simple model which incorporates the dependence of the water- quality-ratio on the entrance porewidths. Common degrees of heterogeneity may lead to significant changes in the injectivity decline, which cannot be described by conventional models of uniform wells. Early damage rates may be orders of magnitude larger than expected and wells with large initial skins are prone to having their half-lifes within this early region. Due to the resulting nonlinearities, extrapolations from test-injections may lead to wrong conclusions and it is usually not possible to predict the half-life by the conventional use of a single value for the water-quality-ratio. P. 631

The Ad5 E1A database is a listing of mutations affecting the early region 1A (E1A) proteins of human adenovirus type 5. The database contains the name of the mutation, the nucleic acid sequence changes, the resulting alterations in amino acid sequence and reference. Additional notes and references are provided on the effect of each mutation on E1A function. The database is contained within the Adenovirus 5 E1A page on the World Wide Web at: http://www.geocities.com/CapeCanaveral/Hangar /2541/

We thank Dr. Gary Ketner (Baltimore, Maryland, U.S.A.) for providing us with many adenoviral E4 deletants, and the W162 cell line. We also thank Dr. P. Boulanger (Montpellier, France) for providing us with antibodies raised against the adenoviral fiber protein, Dr. T. Shenk (Princeton, New Jersey, U.S.A.) and Dr. P. Hearing (Stony Brook, New York, U.S.A.) for their kind gift of antibodies raised against the E4 gene products. We thank A. Gillardeaux, M. Lepeut, I. Mahfouz and C. Jullien for excellent technical assistance, Dr. J.M. Guillaume for the production of viral stocks, and Dr. M.Lakich for critical reading of the manuscript. This work was supported by Bioavenir (Rhone-Poulenc and French Ministry of Research and Industry).

The human polyomaviruses BK (BKV) and JC (JCV) are ubiquitous in human populations and have a worldwide distribution.(1) They are oncogenic in rodents and monkeys and transform cells in vitro to a neoplastic phenotype. For all these reasons, BKV and JCV have been considered possible candidates in the etiology of human tumors. Association of BKV, but not of JCV, with human tumors has been described, although a formal proof for an etiological role of BKV in human oncogenesis is still lacking. SV40, which is not a ubiquitous human virus, has also been sporadically detected in human tumors. In this chapter, we consider their general characteristics, the natural history of infection, experimental transformation and oncogenicity by BKV and JCV, as well as the evidence linking BKV, JCV, and SV40 to human neoplasia.