www.LCaccess—global directory of lci resources

LCAccess is a U.S. Environmental Protection Agency sponsored web-site intended to promote the use of Life Cycle Assessments in business decision-making by facilitating access to data sources useful in developing a life cycle inventory (LCI). While LCAccess will not itself contain data, it will be a searchable global directory to potential data sources. In additional to directing users to relevant data sources, LCAccess will also serve as central source for LCA information. Development is currently being completed on LCAccess with an expected operational date of winter 2000/2001 for some features of the web-site. The LCI Global Directory is expected be fully functional by the summer of 2001. To find the LCAccess web-site in 2001 go to: www.epa.gov/LCAccess. LCAccess is currently soliciting organizations that have completed LCI/LCA studies to provide their data sources for reference in LCAccess. Inquiries should be directed to the development manager, Mr. Tim Skone (US 703/318-4745) and/or the EPA Sponsor, Ms. Mary Ann Curran (513/569-7782).     

Perspectives of development of immunoprophylaxis in Russia

Analytic materials on prevention of controlled infections in Russia and perspectives for extension of immunoprophylaxis field are presented. It was determined that immunization against pertussis should be expanded. Necessity to include vaccines against hepatitis A, Hib, pneumococcal infection, varicella as well as rotavirus and human papillomavirus infection in National immunization schedule is substantiated. It was noted that introduction of new vaccines will require both increase of funding for immunization and switch on use of combination vaccines containing 4 - 6 components.     

Additive and non-additive effects from a larger spatial scale determine small-scale densities in a web spider <Emphasis Type="Italic">Neriene brongersmai</Emphasis>

We examined 15 populations of Neriene brongersmai, a common sheet-web spider inhabiting cedar forest floor, to find out how density at a small spatial scale (patch level) is determined by processes operating at this scale as well as those from a larger spatial scale (population level). Here we focus on two types of large-scale effects that may influence small-scale density: an additive effect that changes the density at patch level; and a non-additive effect that changes the relationship between the density and its limiting factor at the patch level. ANCOVA showed that patch-level density of this spider was positively correlated with web-site availability at this level, but the density with a given amount of web-site differed among populations (cedar forests), indicating the existence of an additive large-scale effect. Multiple regression analysis showed that web-site availability at a population level explained the additive large-scale effect well, but prey availability and forest size did not. It seemed likely that increased web-site availability may have reduced the mortality of spiders while moving to a new web-site, and hence increased population density. A non-additive large-scale effect was also revealed: i.e. the relationship between density and web-site availability at the patch level tended to be stronger in populations with a greater additive large-scale effect. Higher intraspecific competition for web-sites in these populations appeared to have strengthened this relationship.     

A spider population in flux: selection and abandonment of artificial web-sites and the importance of intraspecific interactions in Lephthyphantes tenuis (Araneae: Linyphiidae) in wheat

Lepthyphantes tenuis, a small sheet-webbuilding linyphiid spider is one of the most abundant spider species of cereal fields in Europe. In the present study we examined the process of web-site selection and web-site tenacity by adult females of this species in a winter wheat field. Spiders were selective in their choice of web-site. Different immigration rates into various manipulated web-sites, in field and laboratory, suggested that structural support and suitable micro-climate (high humidity) are the most important factors in the selection. Small holes dug in the ground were the most favoured web-sites. Web-site occupation was influenced by the presence of other conspecific spiders. Territorial contests occurred between spiders attempting to occupy the same web, these almost invariably led to the take-over of the web when the intruder was heavier. Interference, but also a certain level of tolerance, between spiders within the same web-site but in different webs was suggested by direct and indirect evidence. Many holes supported two or even three spiders in vertically stratified webs. Leaving probability of marked spiders was significantly higher in multiply occupied holes than in holes with a single web. Comparison with the results of a no-interference stochastic model showed that multiple occupancy in nature is less frequent than predicted by the model. There was further evidence for weak extra-web-interference between spiders in that multiple occupancy was even less frequent and overall occupancy was lower in web-sites which were packed close to each other. However, a level of tolerance for crowding is shown by the fact that closely packed hole colonies supported a spider density 13 times higher than in natural web-sites in the field. A marking experiment was carried out to gain information on web-site tenacity (i.e. the length of time a spider spends in a web-site) and abandonment. The average duration of tenacity was less than 2 days. A random loss function gave a good fit to the tenacity distribution and suggested that spiders abandoned web-sites randomly with a fixed leaving probability of c. 0.5. Individual webs were often used consecutively by more than one spider, and some spiders built more than one web in the same web-site. Calculations showed that abandonment is the most frequent leaving mode, while take-over by contest between spiders and disappearance due to destruction were some-what less frequent and equally likely modes of ending tenacity. It is suggested that the apparent contradiction between the selectiveness and competitiveness of spiders for web-sites and the relatively short tenacity observed can be resolved by hypothesising that spiders leave websites soon because they apply the strategy of spreading risk: spiders by frequently moving from one web-site to another distribute their reproductive efforts across several localities. This hypothesis is further supported by changes in web-site preference and ballooning behaviour at the onset of the reproductive stage in L. tenuis.     

Galileo Avionica’s Technologies and Instruments for Planetary Exploration

Several missions for planetary exploration, including comets and asteroids, are ongoing or planned by the European Space Agencies: Rosetta, Venus Express, Bepi Colombo, Dawn, Aurora and all Mars Programme (in its past and next missions) are good examples. The satisfaction of the scientific request for the mentioned programmes calls for the development of new instruments and facilities devoted to investigate the body (planet, asteroid or comet) both remotely and by in situ measurements. The paper is an overview of some instruments for remote sensing and in situ planetary exploration already developed or under study by Galileo Avionica Space & Electro-Optics B.U. (in the following shortened as Galileo Avionica) for both the Italian Space Agency (ASI) and for the European Space Agency (ESA). Main technologies and specifications are outlined; for more detailed information please refer to Galileo Avionica’s web-site at: . *Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

Life cycle heterogeneity in animal models of human papillomavirus-associated disease

Animal papillomaviruses are widely used as models to study papillomavirus infection in humans despite differences in genome organization and tissue tropism. Here, we have investigated the extent to which animal models of papillomavirus infection resemble human disease by comparing the life cycles of 10 different papillomavirus types. Three phases in the life cycles of all viruses were apparent using antibodies that distinguish between early events, the onset of viral genome amplification, and the expression of capsid proteins. The initiation of these phases follows a highly ordered pattern that appears important for the production of virus particles. The viruses examined included canine oral papillomavirus, rabbit oral papillomavirus (ROPV), cottontail rabbit papillomavirus (CRPV), bovine papillomavirus type 1, and human papillomavirus types 1, 2, 11, and 16. Each papillomavirus type showed a distinctive gene expression pattern that could be explained in part by differences in tissue tropism, transmission route, and persistence. As the timing of life cycle events affects the accessibility of viral antigens to the immune system, the ideal model system should resemble human mucosal infection if vaccine design is to be effective. Of the model systems examined here, only ROPV had a tissue tropism and a life cycle organization that resembled those of the human mucosal types. ROPV appears most appropriate for studies of the life cycles of mucosal papillomavirus types and for the development of prophylactic vaccines. The persistence of abortive infections caused by CRPV offers advantages for the development of therapeutic vaccines.     

Conspecific and Heterospecific Attraction: A Mechanism of Web-site Selection Leading to Aggregation Formation by Web-building Spiders

This study investigated whether conspecific and/or heterospecific attraction to silk is a mechanism of web-site selection leading to aggregation formation by two species of web-building spiders, Hypochilus thorelli Marx (Araneae: Hypochilidae) and Achaearanea tepidariorum (C.L. Koch) (Araneac: Theridiidae). We determined that the spatial distribution of these two spiders was clumped and that H. thorelli had a greater tendency to aggregate than did A. tepidariorum. To determine the mechanism responsible for this spatial pattern, we conducted three field experiments. We examined web-site selection by H. thorelli in three contexts: no spiders or webs present (cue removed), vacant webs present, and occupied webs present. In the case where no webs were present, there was no tendency for spiders to choose previously occupied sites as web sites. When vacant webs were present, spiders chose to occupy the vacant webs. When occupied webs were present, spiders either invaded webs and evicted the owners, or settled adjacent to and attached their webs to those of residents. Various microhabitat variables (height, angle, temperature, humidity, and substrate character of the rock surface) of randomly selected unoccupied sites and the web sites chosen by spiders were compared. There were no detectable differences between web sites and unoccupied sites with respect to any of the variables measured. This leads us to conclude that web-site choice by immigrating spiders was based on the presence of silk rather than other features of the site.     

Severe papillomavirus infection progressing to metastatic squamous cell carcinoma in bone marrow-transplanted X-linked SCID dogs

Canine X-linked severe combined immunodeficiency (XSCID) is due to mutations in the common gamma chain (gammac) gene and is identical clinically and immunologically to human XSCID, making it a true homologue of the human disease. Bone marrow-transplanted (BMT) XSCID dogs not only engraft donor T cells and reconstitute normal T-cell function but, in contrast to the majority of transplanted human XSCID patients, also engraft donor B cells and reconstitute normal humoral immune function. Shortly after our initial report of successful BMT of XSCID dogs, it soon became evident that transplanted XSCID dogs developed late-onset severe chronic cutaneous infections containing a newly described canine papillomavirus. This is analogous to the late-onset cutaneous papillomavirus infection recently described for human XSCID patients following BMT. Of 24 transplanted XSCID dogs followed for at least 1 year post-BMT, 71% developed chronic canine papillomavirus infection. Six of the transplanted dogs that developed cutaneous papillomas were maintained for >3 1/2 years post-BMT for use as breeders. Four of these six dogs (67%) developed invasive squamous cell carcinoma (SCC), with three of the dogs (75%) eventually developing metastatic SCC, an extremely rare consequence of SCC in the dog. This finding raises the question of whether SCC will develop in transplanted human XSCID patients later in life. Canine XSCID therefore provides an ideal animal model with which to study the role of the gammac-dependent signaling pathway in the response to papillomavirus infections and the progression of these viral infections to metastatic SCC.     

An HLA-A2.1-transgenic rabbit model to study immunity to papillomavirus infection

We have established several HLA-A2.1-transgenic rabbit lines to provide a host to study CD8(+) T cell responses during virus infections. HLA-A2.1 protein expression was detected on cell surfaces within various organ tissues. Continuous cultured cells from these transgenic rabbits were capable of presenting both endogenous and exogenous HLA-A2.1-restricted epitopes to an HLA-A2.1-restricted epitope-specific CTL clone. A DNA vaccine containing an HLA-A2.1-restricted human papillomavirus type 16 E7 epitope (amino acid residues 82-90) stimulated epitope-specific CTLs in both PBLs and spleen cells of transgenic rabbits. In addition, vaccinated transgenic rabbits were protected against infection with a mutant cottontail rabbit papillomavirus DNA containing an embedded human papillomavirus type 16 E7/82-90 epitope. Complete protection was achieved using a multivalent epitope DNA vaccine based on epitope selection from cottontail rabbit papillomavirus E1 using MHC class I epitope prediction software. HLA-A2.1-transgenic rabbits will be an important preclinical animal model system to study virus-host interactions and to assess specific targets for immunotherapy.     

Cis-Acting Negative RNA Elements on Papillomavirus Late mRNAs

Papillomaviruses comprise a large number of related small DNA tumor viruses with tropism for squamous epithelial cells. The papillomavirus replication cycle is strictly linked to the differentiation stages of the infected epithelial cells, and the expression of L1 and L2 capsid proteins from the viral late genes is primarily detected in the superficial layers of terminally differentiated cells. Expression of the L1 and L2 genes is blocked in nonterminally differentiated cells and the production of progeny virus is delayed until the infected cell reaches the upper strata of the squamous epithelium. This property presumably aids the papillomavirus to evade the immune surveillance of the host and allows establishment of persistent infections. Late gene expression levels are determined in part by regulatory RNA sequences on the papillomavirus mRNAs. This review focuses primarily on negativecis-acting elements on late papillomavirus mRNAs and their candidatetrans-acting factors. Identification and characterization of these components will contribute to our understanding of the regulated expression of papillomaviruses in mammalian cells.     

BioLayout--an automatic graph layout algorithm for similarity visualization

Graph layout is extensively used in the field of mathematics and computer science, however these ideas and methods have not been extended in a general fashion to the construction of graphs for biological data. To this end, we have implemented a version of the Fruchterman Rheingold graph layout algorithm, extensively modified for the purpose of similarity analysis in biology. This algorithm rapidly and effectively generates clear two (2D) or three-dimensional (3D) graphs representing similarity relationships such as protein sequence similarity. The implementation of the algorithm is general and applicable to most types of similarity information for biological data. AVAILABILITY: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout.     

Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences

Coding information is the main source of heterogeneity (non-randomness) in the sequences of microbial genomes. The heterogeneity corresponds to a cluster structure in triplet distributions of relatively short genomic fragments (200-400 bp). We found a universal 7-cluster structure in microbial genomic sequences and explained its properties. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy. Based on the analysis of 143 completely sequenced bacterial genomes available in Genbank in August 2004, we show that there are four "pure" types of the 7-cluster structure observed. All 143 cluster animated 3D-scatters are collected in a database which is made available on our web-site (http://www.ihes.fr/~zinovyev/7clusters). The findings can be readily introduced into software for gene prediction, sequence alignment or microbial genomes classification.     

mRNA Instability Elements in the Human Papillomavirus Type 16 L2 Coding Region

Human papillomavirus capsid proteins L1 and L2 are detected only in terminally differentiated cells, indicating that expression of the L1 and L2 genes is blocked in dividing cells. The results presented here establish that the human papillomavirus type 16 L2 coding region contains cis-acting inhibitory sequences. When placed downstream of a reporter gene, the human papillomavirus type 16 L2 sequence reduced both mRNA and protein levels in an orientation-dependent manner. Deletion analysis revealed that the L2 sequence contains two cis-acting inhibitory RNA regions. We identified an inhibitory region in the 5′-most 845 nucleotides of L2 that acted by reducing cytoplasmic mRNA stability and a second, weaker inhibitory region in the 3′ end of L2. In contrast, human papillomavirus type 1 L1 and L2 genes did not encode strong inhibitory sequences. This result is consistent with observations of high virus production in human papillomavirus type 1-infected tissue, whereas only low levels of human papillomavirus type 16 virions are detectable in infected epithelium. The presence of inhibitory sequences in the L1 and L2 mRNAs may aid the virus in avoiding the host immunosurveillance and in establishing persistent infections.     

SACS--self-maintaining database of antibody crystal structure information

MOTIVATION: The rapid increase in the number of structures in the Protein Databank (PDB) makes it difficult to find all structures in a given protein class. Automatically-maintained web-based summaries are one solution to this problem. RESULTS: Summary of Antibody Crystal Structures (SACS), a self-maintaining web-site containing summary information on antibody structures in the PDB, is described. Mirrored PDB data are processed automatically using a Make-based system to identify new antibody structures. The PDB header records and sequence data are then parsed to identify a number of features of the structure and the data are stored using eXtensible Markup Language (XML). eXtensible Stylesheet Language: Transformations (XSLT), a new style sheet language for XML, is used to generate Hypertext Markup Language (HTML) pages containing either a one-line summary of every structure or a more detailed page describing a single antibody.     

Inherited MST1 Deficiency Underlies Susceptibility to EV-HPV Infections

Epidermodysplasia verruciformis (EV) is characterized by persistent cutaneous lesions caused by a specific group of related human papillomavirus genotypes (EV-HPVs) in otherwise healthy individuals. Autosomal recessive (AR) EVER1 and EVER2 deficiencies account for two thirds of known cases of EV. AR RHOH deficiency has recently been described in two siblings with EV-HPV infections as well as other infectious and tumoral manifestations. We report here the whole-exome based discovery of AR MST1 deficiency in a 19-year-old patient with a T-cell deficiency associated with EV-HPV, bacterial and fungal infections. MST1 deficiency has recently been described in seven patients from three unrelated kindreds with profound T-cell deficiency and various viral and bacterial infections. The patient was also homozygous for a rare ERCC3 variation. Our findings broaden the clinical range of infections seen in MST1 deficiency and provide a new genetic etiology of susceptibility to EV-HPV infections. Together with the recent discovery of RHOH deficiency, they suggest that T cells are involved in the control of EV-HPVs, at least in some individuals.     

Structural optimization of a retrograde trafficking inhibitor that protects cells from infections by human polyoma- and papillomaviruses

Human polyoma- and papillomaviruses are non-enveloped DNA viruses that cause severe pathologies and mortalities. Under circumstances of immunosuppression, JC polyomavirus causes a fatal demyelinating disease called progressive multifocal leukoencephalopathy (PML) and the BK polyomavirus is the etiological agent of polyomavirus-induced nephropathy and hemorrhagic cystitis. Human papillomavirus type 16, another non-enveloped DNA virus, is associated with the development of cancers in tissues like the uterine cervix and oropharynx. Currently, there are no approved drugs or vaccines to treat or prevent polyomavirus infections. We recently discovered that the small molecule Retro-2^cycl, an inhibitor of host retrograde trafficking, blocked infection by several human and monkey polyomaviruses. Here, we report diversity-oriented syntheses of Retro-2^cycl and evaluation of the resulting analogs using an assay of human cell infections by JC polyomavirus. We defined structure–activity relationships and also discovered analogs with significantly improved potency as suppressors of human polyoma- and papillomavirus infection in vitro. Our findings represent an advance in the development of drug candidates that can broadly protect humans from non-enveloped DNA viruses and toxins that exploit retrograde trafficking as a means for cell entry.     

Confort térmico y el riesgo de infecciones respiratorias en los adultos mayores en la sierra rural del Perú

The objective is to evaluate thermal comfort in the rural highlands of Peru and determine if thermal conditions influence the risk of respiratory infections. The probit regression model is used for this, with the unit of analysis being adults over 60 years of age. The information source is the data from the National Household Survey and the National Service of Meteorology and Hydrology of Peru. In addition, it was possible to monitor the temperature and the interior relative humidity of 4 types of bedrooms with a thermo-hygrometer and compared it with the desired thermal comfort index criterion. The results show that if the air temperature drops on average by one degree (1° C) in the area of residence, the probability of risk of respiratory infections in older adults increases by 0.18, although the relative humidity and the wind speed were not statistically significant at 1% significance level. Finally, the 4 types of bedrooms evaluated lacked the desired thermal comfort and increased the risk of acquiring respiratory infections.     

Risk behaviors for getting HIV infection among the Croatian men who have sex with men in 2007

This survey was conducted with the aim of obtaining the information on the sexual risk behavior of Croatian men who have sex with men (MSM) two years after the first research. There was total of 820 respondents recruited at seven frequent meeting places of Croatian MSM in Zagreb and Rijeka, as well as one gay-oriented web-site. The overall response rate was 17.6% which is 1.4 percentage point less than it was two years ago. The rate of condom use during last anal intercourse was 53.2% and 69% of those who used a lubricant had chosen a correct water-based product which is increase of 15% comparing to the last research. Only 27% of those who had also had sex with women (MSM/MSW) during last 12 months regularly used protection. The results of this research suggest that there are trends in declining of some risk behaviors among Croatian MSM but there is a lot of space for focused and effective prevention activities on increasing the risk perception and reducing risk behaviors.     

Identification of human papillomavirus antigen in a bladder tumor.

Human papillomavirus (HPV) antigen was found in one of six noninfiltrating (grade II) carcinomas of the bladder. The antigen was located in the nuclei of the superficial cells. This virus-bearing tumor occurred in a patient with no known risk factors. The presence of HPV in low-grade urinary lesions seems to be frequent and may reflect the early stages of carcinogenesis; in fact, HPV infections may cause papillomas and carcinomas of the urothelial mucosae as well as the genital mucosae.     

Genital transmission of HPV in a mouse model is potentiated by nonoxynol-9 and inhibited by carrageenan

Genital human papillomavirus (HPV) infection is the most common sexually transmitted infection, and virtually all cases of cervical cancer are attributable to infection by a subset of HPVs (reviewed in ref. 1). Despite the high incidence of HPV infection and the recent development of a prophylactic vaccine that confers protection against some HPV types, many features of HPV infection are poorly understood. It remains worthwhile to consider other interventions against genital HPVs, particularly those that target infections not prevented by the current vaccine. However, productive papillomavirus infection is species- and tissue-restricted, and traditional models use animal papillomaviruses that infect the skin or oral mucosa. Here we report the development of a mouse model of cervicovaginal infection with HPV16 that recapitulates the establishment phase of papillomavirus infection. Transduction of a reporter gene by an HPV16 pseudovirus was characterized by histology and quantified by whole-organ, multispectral imaging. Disruption of the integrity of the stratified or columnar genital epithelium was required for infection, which occurred after deposition of the virus on the basement membrane underlying basal keratinocytes. A widely used vaginal spermicide, nonoxynol-9 (N-9), greatly increased susceptibility to infection. In contrast, carrageenan, a polysaccharide present in some vaginal lubricants, prevented infection even in the presence of N-9, suggesting that carrageenan might serve as an effective topical HPV microbicide.