bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of River‐Engineering Practices on the Conservation Interest and Water Quality in the Land Yeo, England
Authors: Smith M. , Iwugo K. , Marriott S.
Published: July 2007

The environmental quality of many rivers on the Somerset Levels and Moors has been reduced because of past river‐engineering practices and changes in land use. A new holistic and restorative approach to river management is now helping to improve the quality of aquatic ecosystems. This paper presents the results of a study which assessed the impact of past river and floodplain management on the Land Yeo, Somerset, with the objective of recommending measures for future management. The main findings are that (a) the ecological interest of the river has been reduced due to channel re‐sectioning and flow diversion, and (b) the flow diversion is also causing water‐quality problems such as dissolved‐oxygen reduction. Most of this degradation could be reversed by the adoption of a number of channel and riparian‐enhancement measures and by revising the annual maintenance programme.
Sustainable Urban‐Drainage Systems and Catchment Planning
Authors: Ellis J. B. , D'Arcy B. J. , Chatfield P. R.
Published: July 2007

Partnership initiatives to address the problem of diffuse pollution from impermeable surface runoff within urban catchments are reviewed, with particular reference to mutual stakeholder duties and interests which are vested in the regulatory agencies, planning authorities, developers, water companies and highway agencies within the UK. The role of ‘sustainable urban‐drainage systems’within integrated catchment‐based approaches is considered in the context of the requirements of the EU Water Framework Directive and strategic river‐basin management planning.
MODELLING THE IMPACT OF CLIMATE CHANGE ON DOMESTIC WATER DEMAND
Authors: Goodchild C. W.
Published: July 2007

This report paper examines current domestic water demand elasticity, with weather variables, as an aid to assessing the potential impact of climate change on domestic water demand. An empirical model of the relationship between summer domestic water demand and concurrent weather under current climatic and socio‐economic conditions is developed and then applied to weather data which have been produced for 2020AD climate scenarios. The model is based on data for the Essex area supplied by Essex and Suffolk Water. The results suggest an increase in summer seven‐day average domestic‐water demand of 3.3 l/hd. d (range 1.37–5.72 l/hd. d), in addition to an increase in the frequency of large demand events. The analysis forms the basis of a wider exposition, examining future domestic water demand under varying climate‐change scenarios.
SEQUENCING BATCH REACTORS: A REVIEW
Authors: Boon A. G.
Published: July 2007

Sewage treatment using the activated‐sludge process evolved from the fill‐and‐draw system which was developed by Ardern and Lockett in 1914; the sequencing batch reactor is a modern development of this system. Its success is due to modern technology, particularly the programmable logic controller which controls operational sequences. The process has a single rectangular reaction tank where the various sequences of wastewater fill and aeration, activated‐sludge settlement and effluent decanting are carried out.

This paper reviews the sequencing batch reactor compared with conventional activated sludge, and explains (a) the similarities and differences, (b) the circumstances in which the system is likely to be cost competitive, and (c) modifications that could increase the effectiveness of sequencing batch‐ reactor systems in the future.
BIOFILM FORMATION IN GRANULAR‐BED FILTERS
Authors: Kaur P. , Fitzpatrick C. S. B. , Kerr C.
Published: July 2007

A high microbiological quality of drinking water must be ensured to protect public health. The filtration techniques that are used in treating drinking water play an important role; however, a biofilm can form on granular‐media filters and the accumulated bacteria can slough off and enter the filtered water.

The aim of this research was to examine (a) the potential for biofilm formation and detachment from filter sand, and (b) the effect of different backwash regimes on biofilm removal. During the operation of the filter, bacteria became attached to the sand media, particularly in the top 30 mm of the filter bed. A water‐only backwash at 20% and 40% bed expansion demonstrated poor removal of biofilm throughout the depth of the bed. Collapse‐pulsing is a more efficient method and results in a reduction in the number of bacteria in the filtered water.
BENEFITS OF BIOSOLIDS TO SOIL QUALITY AND FERTILITY
Authors: Chambers B. J. , Nicholson F. A. , Aitken M. , Cartmell E. , Rowlands C.
Published: July 2007

Research in the UK on the beneficial aspects of biosolids additions to land has primarily concentrated on nitrogen and phosphorus supply. Biosolids have other beneficial effects on soil through the addition of organic matter and other plant nutrients such as sulphur, magnesium and sodium. This study evaluates the effects of biosolids additions on soil quality and fertility at seven established field experimental sites where biosolids have been applied for at least four years. These additions influenced several physical properties of the soil, increasing topsoil water‐infiltration rates, plant‐available water supply on a light sandy soil, soil porosity and bearing strength. There were also increases in the level of plant‐available sulphur, magnesium, copper and boron. Liquid digested biosolids applications also increased the concentrations of major nutrients in grass.
LAND USE AND FLOOD RISK THROUGH CATCHMENT FLOOD‐MANAGEMENT PLANS
Authors: Burton A. J. R. , Shepard M. A. , Riddell K. J.
Published: July 2007

Catchment Flood Management Plans involve a high‐level assessment of current flood risk and attempt to demonstrate how this risk could change with time. An influencing factor will be the changes to rural and urban land use on catchment hydraulics. By assessing a range of land use and urban‐growth scenarios catchment wide, a ‘catchment flood management plan’ can demonstrate the cumulative effect on downstream flood‐risk areas. ‘Catchment flood management plan’ methods also indicate how long‐term land‐use and climate changes can expose new areas to more frequent flooding. Techniques to assess these issues, up to a 50‐year horizon, have been established as part of these pilot studies. In addition to briefly describing how land‐use concerns are integrated into such concepts, this paper outlines how flood‐management planning must evolve as a dynamic tool, to fulfil an on‐going requirement for future development assessment.
PLANNING FOR FLOOD RISK IN THE FENS
Authors: Williams S. , Worth D.
Published: July 2007

The fens of eastern England rely on flood defences for their existence, and planning for flood risk has always had a high priority. A new focus was given with the issue of Planning Policy Guidance 25, and this paper presents experience from a Strategic Flood Risk Assessment of South Holland District, in Lincolnshire. The assessment pioneered the examination of fenland flood risk in terms of risk zones related to flood hazard and standard of protection. Methods for evaluating the risk zones are described; they consider flooding from embanked rivers which are subject to tide locking, internal drainage systems, tide level and wave action. The methods would be appropriate for many lowland areas of the UK where conventional flood analysis cannot be used.
SOUTH‐EAST HOUSING DEVELOPMENT — THE QUEST FOR SUSTAINABILITY: WATER AND SEWERAGE NEEDS
Authors: Evans S. G. , Spillett P. B. , Colquhoun K.
Published: July 2007

In March 2000, a document entitled Draft Regional Planning Guidance for the South East was published with the primary aim of providing a regional framework for the preparation of development plans to the year 2016.

This paper discusses the potential effects for the water industry of SERPLAN’s predicted levels of housing growth on water resources, sewage treatment and the environment. The need for sustainable development with the competing pressures of water‐resource limitation, changing regulation, increasing demand and the environment, are discussed. Thames Water’s scale of operations is described together with the range of measures aimed at managing the reasonable demands of customers, consistent with achieving sustainable growth. Basingstoke is described as a wastewater case study, highlighting the problem in fulfilling the sewerage undertaker’s statutory duties in (a) meeting already stringent effluent‐treatment standards which are necessary to maintain and improve river quality, and (b) providing the necessary infrastructure for an area which is earmarked for continuing development.
A HORIZONTAL WELLPOINT AS A LOW‐IMPACT WATER SOURCE IN A DUNE‐SANDS AQUIFER
Authors: Brassington F. C. , Preene M.
Published: July 2007

A horizontal wellpoint groundwater source was constructed to supply irrigation water to a golf course from a coastal dune‐sands aquifer in an area which has vulnerable wetland habitats of European importance. The source was designed to abstract the required quantities with less drawdown, compared with that from a conventional vertical wellpoint system, thus reducing any potential threat to the nature‐conservation sites. Pump testing of the source showed that the yield was more than adequate to meet the needs of the Golf Club and to allow efficient operation of the computer‐controlled course irrigation system. Data from observation wells indicated that there was no drawdown beyond the golf‐course boundaries and none of the nature‐conservation sites would be affected. The horizontal wellpoint method, which has not been widely applied in the UK, could have wider applications for irrigation water users who need to abstract water from shallow aquifers.
CLIMATE‐CHANGE IMPACTS ON RIVER FLOWS IN BRITAIN: THE UKCIPO2 SCENARIOS
Authors: Arnell N. W.
Published: July 2007

This paper describes the implications of the UKCIPO2 climate‐change scenarios for river flows in Britain, focusing on mean monthly runoff and Q95 (i.e. the flow which is exceeded for 95% of the time). By the 2020s. mean summer flows will be about 30% lower than the 1961–1990 mean and Q95 will be reduced by approximately 25%. Percentage reductions are particularly large in southern and eastern England. Mean winter flows are modestly increased, with the greatest increases in the north and west. Reductions in the recharge season result in lower flows in groundwater‐dominated catchments throughout the year. The climate‐change signal is larger than natural multi‐decadal variability ‐ even by the 2020s. This natural variability can add +/‐ 5% to the changes in Q95 due to climate change.

Changes resulting from the UKCIPO2 scenarios are (a) more extreme during summer than those resulting from earlier climate‐change scenarios, showing considerably greater flow reductions, and (b) at the drier end of the range in changes arising from the application of scenarios based on other coarser‐resolution climate models.
Glomerular sieving of three neutral polysaccharides, polyethylene oxide and bikunin in rat. Effects of molecular size and conformation
Authors: Asgeirsson D. , Venturoli D. , Fries E. , Rippe B. , Rippe C.
Published: July 2007

Aim:  Polysaccharides and many other non‐protein polymers generally have a more open, flexible and asymmetrical structure compared with globular proteins. For a given molecular weight (MW), the Stokes–Einstein radius (ae) of the following polymers increases in the order: Ficoll < dextran ≤ pullulan < polyethylene oxide (PEO). We have tested the hypothesis that such an increase in ‘molecular extension’ will increase the molecule’s glomerular permeability. Thus, we investigated the glomerular sieving coefficients (θ) of the mentioned polymers and of the negatively charged and extended protein bikunin.

Methods:  In anaesthetized Wistar rats, glomerular sieving curves were generated for each FITC‐labelled polymer from their respective concentration in urine and plasma, determined by size exclusion chromatography. The θ for bikunin was measured using a tissue uptake technique.

Results:  For a molecule of ae = 55 Å (cf. IgG), θ increased in the order: Ficoll (0.00035 ± 0.000013) < dextran (0.022 ± 0.0029) < pullulan (0.033 ± 0.0024) < PEO (0.12 ± 0.0055). For ae = 36 Å (cf. albumin) the order was: Ficoll (0.076 ± 0.0061) < dextran (0.45 ± 0.037) = pullulan (0.45 ± 0.021) < PEO (0.65 ± 0.0076). θ for bikunin (0.089 ± 0.0045) was 150 times higher than that of albumin, having an equivalent ae and net negative charge.

Conclusion:  From these results it is concluded that for flexible and asymmetric macromolecules, their degree of glomerular hyperpermeability is proportional to their degree of ‘molecular extension’. Thus, compared with globular proteins, the polysaccharides investigated, including Ficoll, were found to be hyperpermeable across the glomerular filter in vivo.
Fish cardiac sodium channels are tetrodotoxin sensitive
Authors: Haverinen J. , Hassinen M. , Vornanen M.
Published: July 2007

Aim:  Sodium current (INa) of the mammalian heart is resistant to tetrodotoxin (TTX) due to low TTX affinity of the cardiac sodium channel (Nav) isoform Nav1.5. To test applicability of this finding to other vertebrates, TTX sensitivity of the fish cardiac INa and its molecular identity were examined.

Methods:  Molecular cloning and whole‐cell patch‐clamp were used to examine α‐subunit composition and TTX inhibition of the rainbow trout (Oncorhynchus mykiss) cardiac Nav respectively.

Results:  I
Na of the trout heart is about 1000 times more sensitive to TTX (IC50 = 1.8–2 nm) than the mammalian cardiac INa and it is produced by three Navα‐subunits which are orthologs to mammalian skeletal muscle Nav1.4, cardiac Nav1.5 and peripheral nervous system Nav1.6 isoforms respectively. Oncorhynchus mykiss (om) omNav1.4a is the predominant isoform of the trout heart accounting for over 80% of the Nav transcripts, while omNav1.5a forms about 18% and omNav1.6a only 0.1% of the transcripts. OmNav1.4a and omNav1.6a have aromatic amino acids, phenylalanine and tyrosine, respectively, in the critical position 401 of the TTX binding site of the domain I, which confers their high TTX sensitivity. More surprisingly, omNav1.5a also has an aromatic tyrosine in this position, instead of the cysteine of the mammalian TTX‐resistant Nav1.5.

Conclusions:  The ortholog of the mammalian skeletal muscle isoform, omNav1.4a, is the predominant Navα‐subunit in the trout heart, and all trout cardiac isoforms have an aromatic residue in position 401 rendering the fish cardiac INa highly sensitive to TTX.
Malignancies in β‐thalassemia patients: a single‐center experience and a concise review of the literature
Authors: BENETATOS L. , ALYMARA V. , VASSOU A. , BOURANTAS K. L.
Published: July 2007

Thalassemia represents the world's most common monogenic disease, characterized by absence of or decreased globin chain production. The lifespan of thalassemia patients has been extended as a result of current supportive treatment. We report three cases of cancer (non‐Hodgkin lymphoma, Hodgkin disease, and seminoma) in thalassemic patients. Factors that may contribute to the pathogenesis of cancer seem to be infections and iron overload through mechanisms of oxidative damage; immunomodulation or coexistence of the two diseases may only be coincidental.
Pneumococcal septic arthritis as the initial presentation of multiple myeloma
Authors: SUMRALL A. , MUZNY C. , BELL J. , DREILING B.
Published: July 2007

Septic arthritis induced by Streptococcus pneumoniae is an uncommon manifestation of pneumococcal infection. Pneumococcus has been identified as the inciting pathogen in only 6% of cases of septic arthritis in recent retrospective studies (Ross et al., 2003). Approximately 50% of patients with pneumococcal septic arthritis have a preceding or concurrent extra‐articular focus of infection. The septic joint evolves from hematogenous seeding of the highly vascular synovial membrane by bacteria. Polyarticular disease occurs in only approximately 36% of patients. Most pneumococcal septic arthritis occurs with coexistant joint disease, prosthesis, alcoholism, HIV infection, or rheumatoid arthritis (Baraboutis & Skoutelis, 2004; Raad & Peacock, 2004). We report a case of polyarticular septic arthritis as the first manifestation of an underlying disease. Our literature review discloses that this is the first reported case of multiple myeloma initially presenting as pneumococcal septic arthritis in the USA and the third internationally (Cuesta et al., 1992; Renou et al., 2007).
International Association of Geoanalysts' Protocol for the Certification of Geological and Environmental Reference Materials: A Supplement
Authors: Kane Jean S. , Potts Philip J. , Meisel Thomas , Wiedenbeck Michael
Published: July 2007

The International Association of Geoanalysts (IAG) published a protocol for the certification of reference materials in close accord with the International Organisation for Standardisation (ISO) guidelines (Kane et al. 2003). This article supplements that protocol, providing additional discussion of best approaches for pre‐selecting laboratories for participation in certification projects. This discussion also makes a distinction between inter‐laboratory certifications, where n = 15 is the general standard, and expert laboratory certifications, where a much smaller number of laboratories will be deemed qualified to provide data of the quality needed for certification.
The Scientific Research Potential of Virtual Worlds
Authors: Bainbridge William Sims
Published: July 2007

Online virtual worlds, electronic environments where people can work and interact in a somewhat realistic manner, have great potential as sites for research in the social, behavioral, and economic sciences, as well as in human-centered computer science. This article uses Second Life and World of Warcraft as two very different examples of current virtual worlds that foreshadow future developments, introducing a number of research methodologies that scientists are now exploring, including formal experimentation, observational ethnography, and quantitative analysis of economic markets or social networks.
Yersinia pestis
CO92Δ
yopH
Is a Potent Live, Attenuated Plague Vaccine
Authors: Bubeck Sarah S. , Dube Peter H.
Published: July 2007

An in-frame deletion of the
yopH
gene in
Yersinia pestis
CO92 attenuates virulence in both bubonic and pneumonic plague models. When it is used as a live, attenuated vaccine, CO92Δ
yopH
provides a high degree of protection from parental and respiratory challenge with
Y. pestis
CO92.
Vibrio vulnificus
Typing Based on Simple Sequence Repeats: Insights into the Biotype 3 Group
Authors: Broza Yoav Y. , Danin-Poleg Yael , Lerner Larisa , Broza Meir , Kashi Yechezkel
Published: July 2007

Vibrio vulnificus
is an opportunistic, highly invasive human pathogen with worldwide distribution.
V. vulnificus
strains are commonly divided into three biochemical groups (biotypes), most members of which are pathogenic. Simple sequence repeats (SSR) provide a source of high-level genomic polymorphism used in bacterial typing. Here, we describe the use of variations in mutable SSR loci for accurate and rapid genotyping of
V. vulnificus
. An in silico screen of the genomes of two
V. vulnificus
strains revealed thousands of SSR tracts. Twelve SSR with core motifs longer than 5 bp in a panel of 32 characterized and 56 other
V. vulnificus
isolates, including both clinical and environmental isolates from all three biotypes, were tested for polymorphism. All tested SSR were polymorphic, and diversity indices ranged from 0.17 to 0.90, allowing a high degree of discrimination among isolates (27 of 32 characterized isolates). Genetic analysis of the SSR data resulted in the clear distinction of isolates that belong to the highly virulent biotype 3 group. Despite the clonal nature of this new group, SSR analysis demonstrated high-level discriminatory power within the biotype 3 group, as opposed to other molecular methods that failed to differentiate these isolates. Thus, SSR are suitable for rapid typing and classification of
V. vulnificus
strains by high-throughput capillary electrophoresis methods. SSR (≥5 bp) by their nature enable the identification of variations occurring on a small scale and, therefore, may provide new insights into the newly emerged biotype 3 group of
V. vulnificus
and may be used as an efficient tool in epidemiological studies.
Electron Microscopy Observation of Human Bocavirus (HBoV) in Nasopharyngeal Samples from HBoV-Infected Children
Authors: Brieu Natalie , Gay Bernard , Segondy Michel , Foulongne Vincent
Published: July 2007

The newly identified human bocavirus is frequently detected by molecular techniques in respiratory samples from children with respiratory tract infections, but virions have not been observed so far. We report the electron microscopy observation of viral particles in nasopharyngeal aspirates previously found to be positive for human bocavirus DNA. The virions presented the expected structural characteristics of a
Parvoviridae
family member.
DNA Pyrosequencing-Based Bacterial Pathogen Identification in a Pediatric Hospital Setting
Authors: Luna Ruth Ann , Fasciano Lea R. , Jones Shaunte C. , Boyanton Bobby L. , Ton Trang T. , Versalovic James
Published: July 2007

Sole reliance on biochemical methods can limit the clinical microbiology laboratory's ability to identify bacterial pathogens. This study describes the incorporation of DNA pyrosequencing-based identification for routine pathogen identification of atypical clinical isolates in a large children's hospital. The assay capitalized on the highly conserved nature of 16S rRNA genes by positioning amplification and sequencing primers in conserved target sequences flanking the variable V1 and V3 regions. A total of 414 isolates of 312 pediatric patients were tested by DNA pyrosequencing during the time period from December 2003 to July 2006. Seventy-eight different genera were specified by DNA pyrosequencing, and isolates were derived from diverse specimen types. By integrating DNA sequencing of bacterial pathogens with conventional microbiologic methods, isolates that lacked a definitive identification by biochemical testing yielded genus- or species-level identifications in approximately 90% of cases by pyrosequencing. Improvements incorporated into the assay process during the period of clinical testing included software enhancements, improvements in sequencing reagents, and refinements in database search strategies. Coupled with isolation by bacteriologic culture and biochemical testing, DNA pyrosequencing-based bacterial identification was a valuable tool that markedly improved bacterial pathogen identification in a pediatric hospital setting.
Catheter-Related Fungemia Due to Fluconazole-Resistant
Candida nivariensis
Authors: Fujita Shin-ichi , Senda Yasuko , Okusi Tikako , Ota Yumi , Takada Hideaki , Yamada Kazunori , Kawano Mitsuhiro
Published: July 2007

We report on a case of fungemia due to fluconazole-resistant
Candida nivariensis
(MIC, ≥128 μg/ml). Internal transcribed spacer PCR followed by microchip gel electrophoresis with a blood culture that tested positive revealed a unique pattern different from those of other pathogenic yeasts.
Binding of Kaposi's Sarcoma-Associated Herpesvirus K-bZIP to Interferon-Responsive Factor 3 Elements Modulates Antiviral Gene Expression
Authors: Lefort Sylvain , Soucy-Faulkner Anton , Grandvaux Nathalie , Flamand Louis
Published: July 2007

Kaposi's sarcoma-associated herpesvirus encodes numerous regulatory proteins capable of modulating viral and cellular gene expression and affecting host cell functions. K-bZIP, a leucine zipper-containing transcription factor encoded by ORFK8, is one such protein. During infection, transcription of the ORFK8 early gene is turned on by the immediate-early replication and transcription factor activator (RTA). One described function of the K-bZIP nuclear protein is to interact with and repress RTA-mediated transactivation of viral promoters, including that of the
K8
gene. In the present work, we provide evidence that the expression of K-bZIP results in the activation of the
ifn
-β gene. Of interest,
ifn
-β gene activation by K-bZIP is independent of interferon (IFN)-responsive factor 3 (IRF-3) and nuclear factor κB (NF-κB) activation. Using a DNA binding affinity assay and electromobility shift assay, we report that K-bZIP binds efficiently to the PRDIII-I region of the beta IFN (IFN-β) promoter, and, in doing so, it prevents the attachment of activated IRF-3 but not that of NF-κB or ATF2/c-Jun to the IFN-β promoter sequence. As a consequence,
ifn
-β gene activation in response to IFN inducers such as Sendai virus infection or expression of retinoic acid-inducible gene I, mitochondrial antiviral signaling protein, or TANK-binding kinase 1 (TBK-1) is severely impaired (>90%) by the presence of K-bZIP. K-bZIP also prevents the activation of RANTES and CXCL11, whose promoters are also regulated by IRF-3. Lysine 158 (target for SUMO conjugation), threonine 111, and serine 167 (targets for phosphorylation) mutants of K-bZIP were equally effective as wild-type K-bZIP in mediating the repression of TBK-1-activated
ifn
-β gene expression. Lastly, the overexpression of CREB binding protein could not reverse the K-bZIP repression of TBK-1-activated
ifn
-β gene expression. In all, our results indicate that K-bZIP binds directly to the PRDIII-I region of the IFN-β promoter and, as a consequence, causes a low level of
ifn
-β gene transcription. In doing so, K-bZIP prevents IRF-3 from binding to the IFN-β promoter and precludes the formation of the enhanceosome, which is required for maximal
ifn
-β gene transcription. A new role for K-bZIP as a protein involved in immune evasion is therefore uncovered.
Emerin Is Hyperphosphorylated and Redistributed in Herpes Simplex Virus Type 1-Infected Cells in a Manner Dependent on both UL34 and US3
Authors: Leach Natalie , Bjerke Susan L. , Christensen Desire K. , Bouchard Jacques M. , Mou Fan , Park Richard , Baines Joel , Haraguchi Tokuko , Roller Richard J.
Published: July 2007

Cells infected with wild-type herpes simplex virus type 1 (HSV-1) show disruption of the organization of the nuclear lamina that underlies the nuclear envelope. This disruption is reflected in changes in the localization and phosphorylation of lamin proteins. Here, we show that HSV-1 infection causes relocalization of the LEM domain protein emerin. In cells infected with wild-type virus, emerin becomes more mobile in the nuclear membrane, and in cells infected with viruses that fail to express UL34 protein (pUL34) and US3 protein (pUS3), emerin no longer colocalizes with lamins, suggesting that infection causes a loss of connection between emerin and the lamina. Infection causes hyperphosphorylation of emerin in a manner dependent upon both pUL34 and pUS3. Some emerin hyperphosphorylation can be inhibited by the protein kinase Cδ (PKCδ) inhibitor rottlerin. Emerin and pUL34 interact physically, as shown by pull-down and coimmunoprecipitation assays. Emerin expression is not, however, necessary for infection, since virus growth is not impaired in cells derived from emerin-null transgenic mice. The results suggest a model in which pUS3 and PKCδ that has been recruited by pUL34 hyperphosphorylate emerin, leading to disruption of its connections with lamin proteins and contributing to the disruption of the nuclear lamina. Changes in emerin localization, nuclear shape, and lamin organization characteristic of cells infected with wild-type HSV-1 also occur in cells infected with recombinant virus that does not make viral capsids, suggesting that these changes occur independently of capsid envelopment.
Molecular Profiling of Ovine Prion Diseases by Using Thermolysin-Resistant PrP
Sc
and Endogenous C2 PrP Fragments
Authors: Owen Jonathan P. , Rees Helen C. , Maddison Ben C. , Terry Linda A. , Thorne Leigh , Jackman Roy , Whitelam Garry C. , Gough Kevin C.
Published: July 2007

Disease-associated PrP fragments produced upon in vitro or in vivo proteolysis can provide significant insight into the causal strain of prion disease. Here we describe a novel molecular strain typing assay that used thermolysin digestion of caudal medulla samples to produce PrP
res
signatures on Western blots that readily distinguished experimental sheep bovine spongiform encephalopathy (BSE) from classical scrapie. Furthermore, the accumulation of such PrP
res
species within the cerebellum also appeared to be dependent upon the transmissible spongiform encephalopathy (TSE) strain, allowing discrimination between two experimental strains of scrapie and grouping of natural scrapie isolates into two profiles. The occurrence of endogenously produced PrP fragments, namely, glycosylated and unglycosylated C2, within different central nervous system (CNS) regions is also described; this is the first detailed description of such scrapie-associated fragments within a natural host. The advent of C2 fragments within defined CNS regions, compared between BSE and scrapie cases and also between two experimental scrapie strains, appeared to be largely dependent upon the TSE strain. The combined analyses of C2 fragments and thermolysin-resistant PrP species within caudal medulla, cerebellum, and spinal cord samples allowed natural scrapie isolates to be separated into four distinct molecular profiles: most isolates produced C2 and PrP
res
in all CNS regions, a second group lacked detectable cerebellar C2 fragments, one isolate lacked both cerebellar PrP
res
and C2, and a further isolate lacked detectable C2 within all three CNS regions and also lacked cerebellar PrP
res
. This CNS region-specific deposition of disease-associated PrP species may reflect the natural heterogeneity of scrapie strains in the sheep population in the United Kingdom.
Adenovirus Virus-Associated RNAII-Derived Small RNAs Are Efficiently Incorporated into the RNA-Induced Silencing Complex and Associate with Polyribosomes
Authors: Xu Ning , Segerman Bo , Zhou Xiaofu , Akusjärvi Göran
Published: July 2007

Adenovirus type 5 encodes two highly structured short RNAs, the virus-associated (VA) RNAI and RNAII. Both are processed by Dicer into small RNAs that are incorporated into the RNA-induced silencing complex (RISC). We show here, by cloning of small RNAs, that approximately 80% of Ago2-containing RISC immunopurified from late-infected cells is associated with VA RNA-derived small RNAs (mivaRNAs). Most surprisingly, VA RNAII, which is expressed at 20-fold lower levels compared to that of VA RNAI, appears to be the preferred substrate for Dicer and accounts for approximately 60% of all small RNAs in RISC. The mivaRNAs are derived from the 3′ strand of the terminal stems of the VA RNAs, with the major fraction of VA RNAII starting at position 138. The small RNAs derived from VA RNAI were more heterogeneous in size, with the two predominant small RNAs starting at positions 137 and 138. Collectively, our results suggest that the mivaRNAs are efficiently used for RISC assembly in late-infected cells. Potentially, they function as miRNAs, regulating translation of cellular mRNAs. In support of this hypothesis, we detected a fraction of the VA RNAII-derived mivaRNAs on polyribosomes.
Persistent Host Markers in Pandemic and H5N1 Influenza Viruses
Authors: Finkelstein David B. , Mukatira Suraj , Mehta Perdeep K. , Obenauer John C. , Su Xiaoping , Webster Robert G. , Naeve Clayton W.
Published: July 2007

Avian influenza viruses have adapted to human hosts, causing pandemics in humans. The key host-specific amino acid mutations required for an avian influenza virus to function in humans are unknown. Through multiple-sequence alignment and statistical testing of each aligned amino acid, we identified markers that discriminate human influenza viruses from avian influenza viruses. We applied strict thresholds to select only markers which are highly preserved in human influenza virus isolates over time. We found that a subset of these persistent host markers exist in all human pandemic influenza virus sequences from 1918, 1957, and 1968, while others are acquired as the virus becomes a seasonal influenza virus. We also show that human H5N1 influenza viruses are significantly more likely to contain the amino acid predominant in human strains for a few persistent host markers than avian H5N1 influenza viruses. This sporadic enrichment of amino acids present in human-hosted viruses may indicate that some H5N1 viruses have made modest adaptations to their new hosts in the recent past. The markers reported here should be useful in monitoring potential pandemic influenza viruses.
Endoribonuclease-Prepared Short Interfering RNAs Induce Effective and Specific Inhibition of Human Immunodeficiency Virus Type 1 Replication
Authors: Gimenez-Barcons Mireia , Clotet Bonaventura , Martinez Miguel Angel
Published: July 2007

Short interfering RNAs (siRNAs) targeting viral or cellular genes can efficiently inhibit human immunodeficiency virus type 1 (HIV-1) replication. Nevertheless, optimal HIV-1 gene silencing by siRNA requires precise complementarity with most of the target sequence. The emergence of mutations in the targeted gene could lead to rapid viral escape from the siRNA. In the present study,
Escherichia coli
endoribonuclease III (RNase III) or mammalian Dicer was used to cleave double-stranded RNA into endoribonuclease-prepared siRNA (esiRNA). esiRNAs generate a variety of siRNAs which can efficiently and specifically target multiple sites in the cognate RNA. esiRNAs targeting the region encoding the HIV-1 reverse transcriptase (RT) reduced viral replication by 90%. The inhibition was dose dependent and sequence specific because several irrelevant esiRNAs did not inhibit HIV-1 replication. Importantly, esiRNAs obtained from the prototypic RT sequence of the HXB2 strain and from highly mutated RT sequences showed similar degrees of viral inhibition, suggesting that the heterogeneous population of esiRNAs could overcome individual mismatches in the RT sequence. Finally, esiRNAs generated by Dicer cleavage were five times more potent than those generated by bacterial RNase III digestion. These results show that esiRNAs are potent HIV-1 inhibitors. Moreover, sequence targets do not need to be highly conserved to reach a high level of viral replication inhibition.
Single Amino Acid Changes in the Nipah and Hendra Virus Attachment Glycoproteins Distinguish EphrinB2 from EphrinB3 Usage
Authors: Negrete Oscar A. , Chu David , Aguilar Hector C. , Lee Benhur
Published: July 2007

The henipaviruses, Nipah virus (NiV) and Hendra virus (HeV), are lethal emerging paramyxoviruses. EphrinB2 and ephrinB3 have been identified as receptors for henipavirus entry. NiV and HeV share similar cellular tropisms and likely use an identical receptor set, although a quantitative comparison of receptor usage by NiV and HeV has not been reported. Here we show that (i) soluble NiV attachment protein G (sNiV-G) bound to cell surface-expressed ephrinB3 with a 30-fold higher affinity than that of sHeV-G, (ii) NiV envelope pseudotyped reporter virus (NiVpp) entered ephrinB3-expressing cells much more efficiently than did HeV pseudotyped particles (HeVpp), and (iii) NiVpp but not HeVpp entry was inhibited efficiently by soluble ephrinB3. These data underscore the finding that NiV uses ephrinB3 more efficiently than does HeV. Henipavirus G chimeric protein analysis implicated residue 507 in the G ectodomain in efficient ephrinB3 usage. Curiously, alternative versions of published HeV-G sequences show variations at residue 507 that can clearly affect ephrinB3 but not ephrinB2 usage. We further defined surrounding mutations (W504A and E505A) that diminished ephrinB3-dependent binding and viral entry without compromising ephrinB2 receptor usage and another mutation (E533Q) that abrogated both ephrinB2 and -B3 usage. Our results suggest that ephrinB2 and -B3 binding determinants on henipavirus G are distinct and dissociable. Global expression analysis showed that ephrinB3, but not ephrinB2, is expressed in the brain stem. Thus, ephrinB3-mediated viral entry and pathology may underlie the severe brain stem neuronal dysfunction seen in fatal Nipah viral encephalitis. Characterizing the determinants of ephrinB2 versus -B3 usage will further our understanding of henipavirus pathogenesis.
The
Mx1
Gene Protects Mice against the Pandemic 1918 and Highly Lethal Human H5N1 Influenza Viruses
Authors: Tumpey Terrence M. , Szretter Kristy J. , Van Hoeven Neal , Katz Jacqueline M. , Kochs Georg , Haller Otto , García-Sastre Adolfo , Staeheli Peter
Published: July 2007

Mice carrying a wild-type
Mx1
gene (
Mx1

+/+

) differ from standard laboratory mice (
Mx1
−/−
) in being highly resistant to infection with common laboratory strains of influenza A virus. We report that
Mx1
also protects mice against the pandemic human 1918 influenza virus and a highly lethal human H5N1 strain from Vietnam. Resistance to H5N1 of
Mx1

+/+

but not
Mx1
−/−
mice was enhanced if the animals were treated with a single dose of exogenous alpha interferon before infection. Thus, the interferon-induced resistance factor Mx1 represents a key component of the murine innate immune system that mediates protection against epidemic and pandemic influenza viruses.
Incorporation of Functional HN-F Glycoprotein-Containing Complexes into Newcastle Disease Virus Is Dependent on Cholesterol and Membrane Lipid Raft Integrity
Authors: Laliberte Jason P. , McGinnes Lori W. , Morrison Trudy G.
Published: July 2007

Newcastle disease virus assembles in plasma membrane domains with properties of membrane lipid rafts, and disruption of these domains by cholesterol extraction with methyl-β-cyclodextrin resulted in the release of virions with irregular protein composition, abnormal particle density, and reduced infectivity (J. P. Laliberte, L. W. McGinnes, M. E. Peeples, and T. G. Morrison, J. Virol. 80:10652-10662, 2006). In the present study, these results were confirmed using Niemann-Pick syndrome type C cells, which are deficient in normal membrane rafts due to mutations affecting cholesterol transport. Furthermore, cholesterol extraction of infected cells resulted in the release of virions that attached to target cells at normal levels but were defective in virus-cell membrane fusion. The reduced fusion capacity of particles released from cholesterol-extracted cells correlated with significant loss of HN-F glycoprotein-containing complexes detected in the virion envelopes of these particles and with detection of cell-associated HN-F protein-containing complexes in extracts of cholesterol-extracted cells. Extraction of cholesterol from purified virions had no effect on virus-cell attachment, virus-cell fusion, particle infectivity, or the levels of glycoprotein-containing complexes. Taken together, these results suggest that cholesterol and membrane rafts are required for the formation or maintenance of HN-F glycoprotein-containing complexes in cells but not the stability of preformed glycoprotein complexes once assembled into virions.
THE PROBLEM OF THE BAND GAP IN LDA CALCULATIONS
Authors: YAKOVKIN I. N. , DOWBEN P. A.
Published: July 2007

In calculating band structure, the local density approximation and density functional theory are widely popular and do reproduce a lot of the basic physics. Regrettably, without some fine tuning, the local density approximation and density functional theory do not generally get the details of the experimental band structure correct, in particular the band gap in semiconductors and insulators is generally found to be too small when compared with experiment. For experimentalists using commercial packages to calculate the electronic structure of materials, some caution is indicated, as some long-standing problems exist with the local density approximation and density functional theory.
AB INITIO STUDY OF NITROGEN-DOPED CARBON NANOTUBES
Authors: YU S. S. , WEN Q. B. , ZHENG W. T. , JIANG Q.
Published: July 2007

Calculations have been made for carbon nanotubes containing substitutional nitrogen impurity atoms using ab initio density functional theory. It is found that the distribution of N atoms depends upon the chirality and diameter of the tube. When two nitrogen atoms are introduced into the (5, 5), (6, 6) and (7, 4) tubes, nitrogen atoms prefer to be adjacent to each other along the circumference, while they tend to be far from each other in other carbon nanotubes. As more nitrogen atoms are incorporated, they prefer to be localized, leading to the broken N – N bond and the interstice is formed in the thin tubes. However, for thick tubes, nitrogen atoms tend to distribute uniformly. It is the finding in this work that the high radial stress plays an important role in nitrogen atom distribution for the thin tubes. For thin N -doped tubes, the major contribution to the structural stabilization comes from the radial stress release after the N – N bond is broken.
Flow perturbation folding in shear zones
Authors: Alsop G. I. , Holdsworth R. E.
Published: July 2007

Variable patterns of displacement in shear zones may result in arcuate fold and fault traces as recognized by Mike Coward and co-workers in the early 1980s. Within such deformation zones, localized perturbations in flow may undergo acceleration (surging flow) or deceleration (slackening flow) with respect to the adjacent regions. Such flow cells may govern the orientation and geometries of folds and fabrics and thereby provide evidence of the scale and nature of deformation associated with heterogeneous flow in the high-strain zones. The length/width ratio of individual flow cells (measured in the direction of flow) may vary from <1 to >1 for situations when flow cells are, respectively, dominated by layer-parallel shear (LPS) or layer-normal shear (LNS). Folds initiating at high angles to transport are associated with LPS, whereas LNS may generate folds with slight clockwise (sinistral LNS) or anticlockwise (dextral LNS) trends relative to flow. Continued progressive deformation may subsequently modify and reduce angular relationships between folds and fabrics, but these geometric obliquities are generally preserved. Using examples from the Moine metasediments of northern Scotland, we show that folding displays predictable geometric patterns that can be related to the development of flow perturbation cells associated with Caledonian ductile thrusting under mid-crustal conditions. The differing relative timing of folds and individual ductile thrusts reflects the complexity of flow cells within ductile imbricates and additionally highlights the progressive foreland-directed propagation of ductile thrusting. These geometric relationships developed during contractional shear are compared with those generated in extensional systems, to provide an overall framework for the study of perturbation patterns. The geometric arrangement of mean fold axial planes about the flow direction results in their intersection forming parallel to the transport direction. This relationship permits transport directions to be calculated via the axial-planar intersection method (AIM), and also allows comparison with other techniques devised primarily for the study of soft-sediment deformation and palaeoslope analysis.
Analysis of a mesoscopic duplex in SW Tuscany, Italy: implications for thrust system development during positive tectonic inversion
Authors: Casini Giulio , Decandia Francesco Antonio , Tavarnelli Enrico
Published: July 2007

The advances in the field of inversion tectonics, pioneered by Mike Coward and co-workers, have shown that many thrust belts originated at the expense of pre-orogenic rift basins that originally had complex extensional architectures. These architectures are reflected by significant lateral thickness and facies changes within the deformed stratigraphic sequences. Although these changes are widely documented from the restoration of balanced sections across thrust fans, they are significantly less well documented from restoration of duplex structures. As a consequence, most available duplex models assume layer-cake stratigraphic sequences. In this contribution a peculiar mesoscopic duplex is described. This structure developed across a single irregular, previously extended quartzite layer of the Arenarie di Poggio al Carpino Formation (Upper Permian-Lower Triassic), during the Late Tertiary orogenic event that led to development of the Apennine chain. Through comparison of the analysed duplex with macroscopic analogues, it is proposed that similar structures may occur on a wide variety of scales, in the Apennines as well as in other orogenic belts.
Structural style and hydrocarbon prospectivity in fold and thrust belts: a global review
Authors: Cooper Mark
Published: July 2007

A statistical analysis of reserves in fold and thrust belts, grouped by their geological attributes, indicates which of the world's fold and thrust belts are the most prolific hydrocarbon provinces. The Zagros Fold Belt contains 490f reserves in fold and thrust belts and has been isolated during the analysis to avoid bias. Excluding the Zagros Fold Belt, most of the reserves are in thin-skinned fold and thrust belts that have no salt detachment or salt seal, are partially buried by syn- or post-orogenic sediments, are sourced by Cretaceous source rocks and underwent their last phase of deformation during the Tertiary. A significant observation is that the six most richly endowed fold and thrust belts have no common set of geological attributes, implying that these fold belts all have different structural characteristics. The implication is that deformation style is a not critical factor for the hydrocarbon endowment of fold and thrust belts; other elements of the petroleum system must be more significant. Other fold and thrust belts may share the structural attributes but the resource-rich fold belts overwhelmingly dominate the total reserves in that group of fold belts. There is nothing intrinsic in fold and thrust belts that differentiates them from other oil- and gas-rich provinces other than the prolific development of potential hydrocarbon traps. Many of the prolific, proven fold and thrust belts still have significant remaining exploration potential as a result of politically challenging access and remote locations.
Au-quartz mineralization near the base of the continental seismogenic zone
Authors: Sibson Richard H.
Published: July 2007

The base of the continental seismogenic zone is defined within individual fault zones by the transition with depth from pressure-sensitive factional (FR) faulting to temperature-sensitive quasi-plastic (QP) ductile shearing. The depth of this FR-QP transition fluctuates principally as a consequence of variations in geothermal gradient and crustal lithology but other factors (e.g. fluid pressure level, strain rate) also play a role. For quartz-dominant and feldspar-dominant lithologies, respectively, it corresponds approximately to isotherms at 300–350°C and
c.
450 °C., defining an undulating transition zone in the mid-crust with a relief of the order of 5–10 km. This transition zone correlates with the greenschist-facies metamorphic environment where the bulk of mesozonal Au-quartz lodes form in mixed continuous-discontinuous shear zones. In areas of crustal convergence and thickening, where fluid release results from prograde metamorphic dehydration, especially at the greenschistamphibolite-facies transition in the middle to deep crust, the seismogenic carapace acts as an upper crustal stress guide and low-permeability lid to overpressured metamorphic fluids migrating through shear zone conduits. Under appropriate combinations of stress and fault architecture in the brittle carapace, substantial fluid volumes may be trapped beneath this elastic lid at sufficient overpressure to generate dilatant fault-fracture meshes discharging episodically by fault-valve action following fault rupture, with permeability locally enhanced by aftershock activity distributed about the rupture zones. Topographic irregularities in the seismic-aseismic transition determine rupture nucleation sites and probably play a critical role in focusing the discharge of overpressured metamorphic fluids into the seismogenic layer. This helps to account for the observed spacing of mesozonal lode systems along transcrustal shear zones.