bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying dominance and deleterious effect on human disease genes
Authors: Osada Naoki , Mano Shuhei , Gojobori Jun
Published: January 2009

Human genes responsible for inherited diseases are important for the understanding of human disease. We investigated the degree of polymorphism and divergence in the human disease genes to elucidate the effect of natural selection on human disease genes. In particular, the effect of disease dominance was incorporated into the analysis. Both dominant disease genes (DDG) and recessive disease genes (RDG) had a higher mutation rate per site and encoded longer proteins than the nondisease genes, which exposed the disease genes to a faster flux of new mutations. Using an unbiased polymorphism dataset, we found that, proportionally, RDG harbor more nonsynonymous polymorphisms compared with DDG. We estimated the selection intensity on the disease genes using polymorphism and divergence data and determined whether the different patterns of polymorphism and divergence between DDG and RDG could be explained by the difference in only dominance. Even after the dominance effect was considered, the selection intensity on RDG was significantly different from DDG, suggesting that the deleterious effect of the dominant and recessive disease mutations are fundamentally different.
The Epstein–Barr virus nuclear antigen-1 promotes genomic instability via induction of reactive oxygen species
Authors: Gruhne Bettina , Sompallae Ramakrishna , Marescotti Diego , Kamranvar Siamak Akbari , Gastaldello Stefano , Masucci Maria G.
Published: January 2009

The Epstein–Barr virus (EBV) nuclear antigen (EBNA)-1 is the only viral protein expressed in all EBV-carrying malignancies, but its contribution to oncogenesis has remained enigmatic. We show that EBNA-1 induces chromosomal aberrations, DNA double-strand breaks, and engagement of the DNA damage response (DDR). These signs of genomic instability are associated with the production of reactive oxygen species (ROS) and are reversed by antioxidants. The catalytic subunit of the leukocyte NADPH oxidase, NOX2/gp91
phox
, is transcriptionally activated in EBNA-1–expressing cells, whereas inactivation of the enzyme by chemical inhibitors or RNAi halts ROS production and DDR. These findings highlight a novel function of EBNA-1 and a possible mechanism by which expression of this viral protein could contribute to malignant transformation and tumor progression.
Optimization of gene expression by natural selection
Authors: Bedford Trevor , Hartl Daniel L.
Published: January 2009

It is generally assumed that stabilizing selection promoting a phenotypic optimum acts to shape variation in quantitative traits across individuals and species. Although gene expression represents an intensively studied molecular phenotype, the extent to which stabilizing selection limits divergence in gene expression remains contentious. In this study, we present a theoretical framework for the study of stabilizing and directional selection using data from between-species divergence of continuous traits. This framework, based upon Brownian motion, is analytically tractable and can be used in maximum-likelihood or Bayesian parameter estimation. We apply this model to gene-expression levels in 7 species of
Drosophila
, and find that gene-expression divergence is substantially curtailed by stabilizing selection. However, we estimate the selective effect,
s
, of gene-expression change to be very small, approximately equal to
Ns
for a change of one standard deviation, where
N
is the effective population size. These findings highlight the power of natural selection to shape phenotype, even when the fitness effects of mutations are in the nearly neutral range.
Measuring the Influence of the BKCa β1 Subunit on Ca2+ Binding to the BKCa Channel
Authors: Sweet Tara-Beth , Cox Daniel H.
Published: January 2009

The large-conductance Ca2+-activated potassium (BKCa) channel of smooth muscle is unusually sensitive to Ca2+ as compared with the BKCa channels of brain and skeletal muscle. This is due to the tissue-specific expression of the BKCa auxiliary subunit β1, whose presence dramatically increases both the potency and efficacy of Ca2+ in promoting channel opening. β1 contains no Ca2+ binding sites of its own, and thus the mechanism by which it increases the BKCa channel's Ca2+ sensitivity has been of some interest. Previously, we demonstrated that β1 stabilizes voltage sensor activation, such that activation occurs at more negative voltages with β1 present. This decreases the work that Ca2+ must do to open the channel and thereby increases the channel's apparent Ca2+ affinity without altering the real affinities of the channel's Ca2+ binding sites. To explain the full effect of β1 on the channel's Ca2+ sensitivity, however, we also proposed that there must be effects of β1 on Ca2+ binding. Here, to test this hypothesis, we have used high-resolution Ca2+ dose–response curves together with binding site–specific mutations to measure the effects of β1 on Ca2+ binding. We find that coexpression of β1 alters Ca2+ binding at both of the BKCa channel's two types of high-affinity Ca2+ binding sites, primarily increasing the affinity of the RCK1 sites when the channel is open and decreasing the affinity of the Ca2+ bowl sites when the channel is closed. Both of these modifications increase the difference in affinity between open and closed, such that Ca2+ binding at either site has a larger effect on channel opening when β1 is present.
Daily Hazard of Acquisition of Methicillin-Resistant Staphylococcus aureus Infection in the Intensive Care Unit
Authors: Marshall Caroline , Spelman Denis , Harrington Glenys , McBryde Emma
Published: January 2009

Objective.

Increasing length of hospital stay is associated with methicillin-resistant Staphylococcus aureus (MRSA) acquisition. The exact risk of becoming colonized with MRSA on a given day has not been clearly elucidated. We determined the hazard of MRSA acquisition in relation to the length of time spent in an intensive care unit in which only standard precautions were used for MRSA-colonized and MRSA-infected patients.

Methods.

This study took place at a tertiary referral hospital intensive care unit in which patients were screened for MRSA at hospital admission, at hospital discharge, and twice weekly during intensive care unit stay. We analyzed the hazard of MRSA acquisition by using a statistical smoothing kernel for hazard with a width of 5 days. Patients were stratified according to age, sex, medical unit, and length of hospital stay.

Results.

Of the patients who were at risk of colonization or infection, 12.8% acquired MRSA. The mean length of stay in the intensive care unit was 7.2 days. The daily hazard of acquiring MRSA was less than 1% at admission to the intensive care unit and increased linearly to more than 2% risk per day by day 12, followed by a leveling out of risk.

Conclusions.

The daily hazard of acquiring MRSA is not constant. This has implications for studies that assume a constant hazard in their analysis and should be considered.
Vertical movements of “escaped” farmed Atlantic salmon (Salmo salar L.)—a simulation study in a western Norwegian fjord
Authors: Skilbrei Ove T. , Holst Jens Christian , Asplin Lars , Holm Marianne
Published: January 2009

Skilbrei, O. T., Holst, J. C., Asplin, L., and Holm, M. 2009. Vertical movements of “escaped” farmed Atlantic salmon (Salmo salar L.)—a simulation study in a western Norwegian fjord. – ICES Journal of Marine Science, 66: 278–288. To study the vertical distribution of fish that had been allowed to escape, farmed Atlantic salmon were tagged with acoustic tags equipped with depth sensors, and then released on five different dates in the course of a year from two fish farms in the Hardanger Fjord in western Norway. Release stimulated the fish to dive to deeper than 15 m during the first hours or days post-release, often down to 50–80 m. However, during the following 4 weeks, most of the escapees spent most of their time above the pycnocline at depths of 0–4 m. The fish were more widely distributed in the water column after release during winter, but still spent most of the time in the cold surface layers. There was a wide range in the vertical distribution of individual fish, and the proportion of detections below 14-m depth ranged from 0 to 90%. There was a significant diurnal cycle in all seasons except midsummer, when the fish were less abundant in the upper layer during daylight, especially on brighter days. The results suggest that salmon diving activity following escape may complicate the recapture of escaped fish at the farm site but that the subsequent tendency of most fish to stay near the surface, virtually irrespective of the time of year, may facilitate recapture.
Asymmetric reproductive isolation during simultaneous reciprocal mating in pulmonates
Authors: Wiwegweaw Amporn , Seki Keiichi , Mori Hiroshi , Asami Takahiro
Published: January 2009

The generality of asymmetric reproductive isolation between reciprocal crosses suggests that the evolution of isolation mechanisms often proceeds in reciprocal asymmetry. In hermaphroditic snails that copulate simultaneously and reciprocally, asymmetry in premating isolation may not be readily detectable because the failure of the symmetric performance of courtship would prevent copulation from occurring. On the other hand, through their prolonged copulation, snails discriminate among mates when exchanging spermatophores for their benefit and thus may exhibit asymmetric reproductive isolation during interspecific mating. However, no clear case of reciprocal asymmetry has been found in reproductive isolation between snail species. Here we show a discrete difference in hybridization success between simultaneous reciprocal copulations between two species of pulmonate snails. Premating isolation ofBradybaena pellucida(BP) andBradybaena similaris(BS) is incomplete in captivity. In interspecific copulation, BP removes its penis without transferring a spermatophore, while BS sires hybrids by inseminating BP. Thus, ‘male’ BP or ‘female’ BS rejects the other individual, while female BP and male BS accept each other, so that the two sexes of either BP or BS oppose each other in mate discrimination. Our results are a clear example of asymmetry in reproductive isolation during simultaneous reciprocal mating between hermaphroditic animals.
Production and perception of communicatory signals in a noisy environment
Authors: Luther David A , Wiley R. Haven
Published: January 2009

Many animals communicate in situations that make it difficult to discriminate a species' signals from those of others. Consequently, coexisting species usually have signals that differ by more than the minimum required to prevent overlap in acoustic features. These gaps between signals might facilitate detection and discrimination of degraded signals in noisy natural conditions. If so, perception of signals should have broader scope than production. We investigated this possibility by studying song production and perception of two species of birds in an especially noisy environment, the Amazonian dawn chorus. With software developed for this study, we digitally synthesized songs of two species, as well as intermediate versions of their songs. Experimental playbacks of these synthesized songs to individuals of both species confirmed that perception (as indicated by responses) was broader than production of songs. We propose that broader perception than production of song promotes communication in noisy situations and limits the similarity between signals of coexisting species.
Iridescent structural colour production in male blue-black grassquit feather barbules: the role of keratin and melanin
Authors: Maia Rafael , Caetano João Victor O , Báo Sônia N , Macedo Regina H
Published: January 2009

Iridescent coloration plays an important role in the visual communication system of many animal taxa. It is known that iridescent structural colours result from layers of materials with different refractive indexes, which in feathers usually are keratin, melanin and air. However, the role of these materials in the production of structural iridescent coloration is still poorly documented. Despite the great interspecific variation in the organization of such structures in bird plumage, melanin layers are usually considered too opaque, suggesting its main role is to delineate the outermost keratin layer and absorb incoherently scattered stray light. We combined spectrometry, electron microscopy and thin-film optical modelling to describe the UV-reflecting iridescent colour of feather barbules of male blue-black grassquits (Volatinia jacarina), characterized by a keratin layer overlying a single melanin layer. Our models indicate that both the keratin and the melanin layers are essential for production of the observed colour, influencing the coherent scattering of light. The melanin layer in some barbules may be thin enough to allow interaction with the underlying keratin; however, individuals usually have, on an average, the minimum number of granules that optimizes absorbance by this layer. Also, we show that altering optical properties of the materials resulted in better-fitting models relative to the empirically measured spectra. These results add to previous findings concerning the influence of melanin in single-layer iridescence, and stress the importance of considering natural variation when characterizing such photonic structures.
Possession of the macrophage-induced gene by isolates of the Mycobacterium avium complex is not associated with significant clinical disease
Authors: Yoon Jong Hyun , Kim Eui-Chong , Kim Jae Seok , Song Eun Young , Yi Jongyoun , Shin Sue
Published: January 2009

TheMycobacterium aviumcomplex (MAC) is the most frequently isolated species among non-tuberculous mycobacteria (NTM) clinical isolates. Physicians pay attention to the differential diagnosis of the disease caused by MAC from tuberculosis because of their similar clinical presentations. Expression of the macrophage-induced gene (mig) is one of the virulence phenotypes in MAC, but it has not been determined whether the presence of themiggene itself has any relationship with clinical disease or whether it is merely a marker for MAC. To uncover the significance of themiggene among MAC clinical isolates, positive cultures from respiratory specimens from patients in a tertiary referral centre were identified by sequencing the 16S rRNA gene. Themiggene was also evaluated using PCR and sequence analysis. The medical records from the patients were reviewed retrospectively. The diagnostic criteria from the American Thoracic Association were adopted for the diagnosis of NTM lung disease. A total of 45 MAC clinical isolates were identified over a period of 1 year. Following 16S rRNA sequencing, all of the 23M. aviumisolates were categorized as sequevar I. Among the 22Mycobacterium intracellulareisolates, 18 strains were identified asM. intracellularesequevar I and the remaining four consisted of one each of sequevars II, III, IV and V. The proportion of cases that fitted the diagnostic criteria of NTM lung disease was 26.7 % (12/45). ThemigPCR results were 100 % positive for the MAC isolates studied, irrespective of their species, sequevar or disease-causing properties. However, following bootstrap analysis of themigsequences, we observed definite grouping betweenM. aviumandM. intracellulare. Thus themiggene is a species-specific marker with distinct sequence diversity between the two speciesM. aviumandM. intracellulare, but there is poor correlation between disease-causing properties and specificmigsequences.
Maternofetal infections due to Eikenella corrodens
Authors: Garnier Fabien , Masson Geoffrey , Bedu Antoine , Masson Philippe , Decroisette Emmanuel , Guigonis Vincent , Fermeaux Véronique , De Barbentane Marie-Christine , Denis François , Ploy Marie-Cécile
Published: January 2009

Eikenella corrodens, a commensal of the human oral cavity, is generally associated with bite wounds and head and neck infections. Neonatal infections are rare. We report two cases of premature birth associated with maternofetal E. corrodens infection.
Vibrio cholerae O1 clinical strains isolated in 1992 in Kolkata with progenitor traits of the 2004 Mozambique variant
Authors: Chatterjee Souvik , Patra Tapas , Ghosh Kausik , Raychoudhuri Amit , Pazhani Gururaja P. , Das Mayukh , Sarkar Banwarilal , Bhadra Rupak K. , Mukhopadhyay Asish K. , Takeda Yoshifumi , Nair G. Balakrish , Ramamurthy Thandavarayan , Nandy Ranjan K.
Published: January 2009

Retrospective analysis led to the detection of twoVibrio choleraevariant O1 strains (VC51 and VC53), which were isolated in 1992 in Kolkata from clinical cases, with identical traits to 2004 Mozambique variant O1 strains. The Mozambique O1 strains that caused a huge outbreak in 2004 have been shown to have phenotypic traits of both classical and El Tor biotypes, and thereby have been reported as variant. Our study demonstrated that two O1 strains isolated in Kolkata during 1992 were of the El Tor background as evidenced by polymyxin B (50 U ml−1) resistance, positivity in Voges–Proskauer reactions and sensitivity to biotype-specific vibrio phages. With the features of classical CTX prophage, localization in the small chromosome, and an absence of RS1 and pTLC, both Mozambique and Kolkata strains appeared to be identical. Furthermore, two Kolkata strains exhibited an identical ribotype to that of the Mozambique variant, displaying ribotype pattern RI that had been assigned to KolkataV. choleraeO1 strains isolated on or before 1992.NotI pulsotype analysis indicated that these 1992 Kolkata strains along with the Mozambique variant O1 belonged to very closely related clones. Considering the chronological events, and the typical identity at the phenotypic and the genotypic level between the two O1 strains isolated during 1992 from Kolkata and during 2004 from Mozambique, we propose that some of the 1992 Kolkata O1 strains might have acted as progenitors for Mozambique variant O1 strains.
CTX-M-14 and CTX-M-15 enzymes are the dominant type of extended-spectrum β-lactamase in clinical isolates of Escherichia coli from Korea
Authors: Song Wonkeun , Lee Hyukmin , Lee Kyungwon , Jeong Seok Hoon , Bae Il Kwon , Kim Jae-Seok , Kwak Hyo-Sun
Published: January 2009

This study was performed to assess the prevalence and genotypes of plasmid-borne extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases in Escherichia coli in Korea. A total of 576 isolates of E. coli was collected from 12 Korean hospitals during May and July 2007. A phenotypic confirmatory test detected ESBLs in 82 (14.2 %) of the 576 E. coli isolates. The most common types of ESBLs identified were CTX-M-14 (n=32) and CTX-M-15 (n=27). The prevalence and diversity of the CTX-M mutants, including CTX-M-15, CTX-M-27 and CTX-M-57, with significant hydrolytic activity against ceftazidime were increased. PCR experiments detected genes encoding plasmid-borne AmpC β-lactamases in 15/56 cefoxitin-intermediate or cefoxitin-resistant isolates, and the most common type of AmpC β-lactamase identified was DHA-1 (n=10). These data suggest that the incidence of ESBLs in E. coli has increased as a result of the dissemination of CTX-M enzymes in Korea. In addition, CTX-M-22, CTX-M-27 and CTX-M-57 have appeared in Korea.
Isolation of the anaerobic intestinal spirochaete Brachyspira pilosicoli from long-term residents and Indonesian visitors to Perth, Western Australia
Authors: Margawani K. Rini , Robertson Ian D. , Hampson David J.
Published: January 2009

Brachyspira pilosicoli is an anaerobic spirochaete that colonizes the large intestine of humans and various species of animals and birds. The spirochaete is an important enteric pathogen of pigs and poultry, but its pathogenic potential in humans is less clear. In the current study, the occurrence of B. pilosicoli in faecal samples from 766 individuals in two different population groups in Perth, Western Australia, was investigated by selective anaerobic culture. Of 586 individuals who were long-term residents of Perth, including children, elderly patients in care and in hospital and individuals with gastrointestinal disease, only one was culture positive. This person had a history of diverticulitis. In comparison, faeces from 17 of 180 (9.4 %) Indonesians who were short- or medium-term visitors to Perth were positive for B. pilosicoli. The culture-positive individuals had been in the city for between 10 days and 4.5 years (median 5 months). Resampling of subsets of the Indonesians indicated that all negative people remained negative and that some positive individuals remained positive after 5 months. Two individuals had pairs of isolates recovered after 4 and 5 months that had the same PFGE types, whilst another individual had isolates with two different PFGE types that were identified 2 months apart. Individuals who were culture-positive were likely to have been either colonized in Indonesia before arriving in Perth or infected in Perth following contact with other culture-positive Indonesians with whom they socialized. Colonization with B. pilosicoli was not significantly associated with clinical signs at the time the individuals were tested, although faeces with wet-clay consistency were 1.5 times more likely (confidence interval 0.55–4.6) than normal faeces to contain B. pilosicoli.
Frequent foamy virus infection in free-living chimpanzees of the Taï National Park (Côte d'Ivoire)
Authors: Morozov Vladimir A. , Leendertz Fabian H. , Junglen Sandra , Boesch Christophe , Pauli Georg , Ellerbrok Heinz
Published: January 2009

Foamy viruses are frequently found in non-human primates and apes in captivity. However, data on simian foamy virus (SFV) infection in apes from the wild are limited. Necropsy specimens were collected from 14 West African chimpanzees (Pan troglodytes verus) from three communities in the Taï National Park, Côte d'Ivoire. PCR analysis revealed SFV-relatedint-andenv-specific sequences in 12/14 chimpanzees. Two young chimpanzees were not infected. Plasma from ‘PCR-positive’ chimpanzees reacted against Pr71/74gagin Western blot analysis. Phylogenetic analysis demonstrated clustering of all analysed sequences with SFVcpz previously identified from the otherP. troglodytes verus, although interestingly the sequences were diverse and no grouping according to a particular animal community was observed. The body compartments of two infected animals were examined and found to contain SFV sequences. Frequent SFV infections in chimpanzees from this area significantly increase the potential risk of zoonotic transmission to rural populations through direct contact, hunting and consumption of bush meat.
Broad, high-magnitude and multifunctional CD4+ and CD8+ T-cell responses elicited by a DNA and modified vaccinia Ankara vaccine containing human immunodeficiency virus type 1 subtype C genes in baboons
Authors: Burgers Wendy A. , Chege Gerald K. , Müller Tracey L. , van Harmelen Joanne H. , Khoury Greg , Shephard Enid G. , Gray Clive M. , Williamson Carolyn , Williamson Anna-Lise
Published: January 2009

Candidate human immunodeficiency virus (HIV) vaccine regimens based on DNA boosted with recombinant modified vaccinia Ankara (MVA) have been in development for some time, and there is evidence for improved immunogenicity of newly developed constructs. This study describes immune responses to candidate DNA and MVA vaccines expressing multiple genes (gag, RT, tat, nef and env) from HIV-1 subtype C in chacma baboons (Papio ursinus). The vaccine regimen induced (i) strong T-cell responses, with a median of 4103 spot forming units per 106 peripheral blood mononuclear cells by gamma interferon (IFN-γ) ELISPOT, (ii) broad T-cell responses targeting all five vaccine-expressed genes, with a median of 12 peptides targeted per animal and without any single protein dominating the response, (iii) balanced CD4+ and CD8+ responses, which produced both IFN-γ and interleukin (IL)-2, including IL-2-only responses not detected by the ELISPOT assay, (iv) vaccine memory, which persisted 1 year after immunization and could be boosted further, despite strong anti-vector responses, and (v) mucosal T-cell responses in iliac and mesenteric lymph nodes in two animals tested. The majority of peptide responses mapped contained epitopes previously identified in human HIV infection, and two high-avidity HIV epitope responses were confirmed, indicating the utility of the baboon model for immunogenicity testing. Together, our data show that a combination of DNA and MVA immunization induced robust, durable, multifunctional CD4+ and CD8+ responses in baboons targeting multiple HIV epitopes that may home to mucosal sites. These candidate vaccines, which are immunogenic in this pre-clinical model, represent an alternative to adenoviral-based vaccines and have been approved for clinical trials.
Subcellular localization and expression of bamboo mosaic virus satellite RNA-encoded protein
Authors: Palani Paramasivan Vijaya , Chiu Morgan , Chen Wei , Wang Ching-Chi , Lin Choy-Chieng , Hsu Chuen-Chi , Cheng Chi-Ping , Chen Chung-Mong , Hsu Yau-Heiu , Lin Na-Sheng
Published: January 2009

The satellite RNA of bamboo mosaic virus (satBaMV) has a single open reading frame encoding a non-structural protein, P20, which facilitates long-distance movement of satBaMV in BaMV and satBaMV co-infected plants. Immunohistochemistry and immunoelectron microscopy revealed that the P20 protein accumulated in the cytoplasm and nuclei in co-infected cells. P20 and the helper virus coat protein (CP) were highly similar in their subcellular localization, except that aggregates of BaMV virions were not labelled with anti-P20 serum. The BaMV CP protein was fairly abundant in mesophyll cells, whilst P20 was more frequently detected in mesophyll cells and vascular tissues. The expression kinetics of the P20 protein was similar to but slightly earlier than that of CP in co-infectedBambusa oldhamiiprotoplasts andNicotiana benthamianaleaves. However, satBaMV-encoded protein levels declined rapidly in the late phase of co-infection. During co-infection, in addition to the intact P20, a low-molecular-mass polypeptide of 16 kDa was identified as a P20 C-terminally truncated product; the possible method of generation of the truncated protein is discussed.
A prairie dog animal model of systemic orthopoxvirus disease using West African and Congo Basin strains of monkeypox virus
Authors: Hutson Christina L. , Olson Victoria A. , Carroll Darin S. , Abel Jason A. , Hughes Christine M. , Braden Zachary H. , Weiss Sonja , Self Joshua , Osorio Jorge E. , Hudson Paul N. , Dillon Michael , Karem Kevin L. , Damon Inger K. , Regnery Russell L.
Published: January 2009

Multiple monkeypox virus (MPXV) animal models have been discussed in previous studies, but no small animal models, nor most non-human primate models, demonstrated the protracted asymptomatic incubation phase seen in systemic human orthopoxvirus illness. Herein, we characterize a black-tailed prairie dog (PD) (Cynomys ludovicianus) model of infection, via intranasal and intradermal exposures, with the two MPXV clades. Daily observations of the animals were made (food consumption, general symptoms, disease presentation), while weights and virus evaluations (ocular, nasal, oropharyngeal, faeces, blood) were obtained/made every third day. Generalized rash became apparent 9–12 days post-infection for all animals. Individual animals demonstrated a range of symptoms consistent with human monkeypox disease. Measurable viraemias and excretas were similar for both clade-representative strains and persisted until at least day 21. Greater morbidity was observed in Congo Basin strain-challenged animals and mortality was observed only in the Congo Basin strain-challenged animals. The PD model is valuable for the study of strain-dependent differences in MPXV. Additionally, the model closely mimics human systemic orthopoxvirus disease and may serve as a valuable non-human surrogate for investigations of antivirals and next generation orthopoxvirus vaccines.
Simian immunodeficiency virus types 1 and 2 (SIV mnd 1 and 2) have different pathogenic potentials in rhesus macaques upon experimental cross-species transmission
Authors: Souquière Sandrine , Onanga Richard , Makuwa Maria , Pandrea Ivona , Ngari Paul , Rouquet Pierre , Bourry Olivier , Kazanji Mirdad , Apetrei Cristian , Simon François , Roques Pierre
Published: January 2009

The mandrill (Mandrillus sphinx) is naturally infected by two types of simian immunodeficiency virus (SIV): SIVmnd types 1 and 2. Both of these viruses cause long-term, non-progressive infections in their natural host despite high plasma viral loads. This study assessed the susceptibility of rhesus macaques to infection by these two types of SIVmnd and compared the virological and basic immunological characteristics of the resulting infections with those observed in natural infection in mandrills. Whilst both SIVmnd types induced similar levels of virus replication during acute infection in both mandrills and macaques, they produced a more pronounced CD4+ T-cell depletion in rhesus macaques that persisted longer during the initial stage of infection. Pro-inflammatory cytokine responses were also induced at higher levels in rhesus macaques early in the infection. During the chronic phase of infection in mandrills, which in this case was followed for up to 2 years after infection, high levels of chronic virus replication did not induce significant changes in CD4+ or CD8+ T-cell counts. In rhesus macaques, the overall chronic virus replication level was lower than in mandrills. At the end of the follow-up period, although the viral loads of SIVmnd-1 and SIVmnd-2 were relatively similar in rhesus macaques, only SIVmnd-1-infected rhesus macaques showed significant CD4+ T-cell depletion, in the context of higher levels of CD4+ and CD8+ T-cell activation, compared with SIVmnd-infected mandrills. The demonstration of the ability of both SIVmnd types to induce persistent infections in rhesus macaques calls for a careful assessment of the potential of these two viruses to emerge as new human pathogens.
Production of protective gamma interferon by natural killer cells during early mouse hepatitis virus infection
Authors: Thirion Gaëtan , Coutelier Jean-Paul
Published: January 2009

Gamma interferon (IFN-γ) plays a major role in the protection against lethal infection with mouse hepatitis virus A59. IFN-γproduction reaches a maximum level 2 days after viral inoculation, especially in liver immune cells. Among these cells, natural killer cells are the major producers of this cytokine. Transfer experiments indicated that the protective role of IFN-γis mediated through a direct effect on cells targeted by the virus rather than through indirect activation of T lymphocytes.
Inhibition of RNA silencing by the coat protein of Pelargonium flower break virus: distinctions from closely related suppressors
Authors: Martínez-Turiño Sandra , Hernández Carmen
Published: January 2009

Viral-derived double-stranded RNAs (dsRNAs) activate RNA silencing, generating small interfering RNAs (siRNAs) which are incorporated into an RNA-induced silencing complex (RISC) that promotes homology-dependent degradation of cognate RNAs. To counteract this, plant viruses express RNA silencing suppressors. Here, we show that the coat protein (CP) of Pelargonium flower break virus (PFBV), a member of the genus Carmovirus, is able to efficiently inhibit RNA silencing. Interestingly, PFBV CP blocked both sense RNA- and dsRNA-triggered RNA silencing and did not preclude generation of siRNAs, which is in contrast with the abilities that have been reported for other carmoviral CPs. We have also found that PFBV CP can bind siRNAs and that this ability correlates with silencing suppression activity and enhancement of potato virus X pathogenicity. Collectively, the results indicate that PFBV CP inhibits RNA silencing by sequestering siRNAs and preventing their incorporation into a RISC, thus behaving similarly to unrelated viral suppressors but dissimilarly to orthologous ones.
Generation of an improved foamy virus vector by dissection of cis-acting sequences
Authors: Wiktorowicz Tatiana , Peters Katrin , Armbruster Nicole , Steinert Andre F. , Rethwilm Axel
Published: January 2009

In contrast to other retroviruses, foamy viruses (FVs) generate their Pol protein precursor independently of the Gag protein from a spliced mRNA. The exact mechanism of Pol protein incorporation into the viral capsid is poorly understood. Previously, we showed that Pol encapsidation critically depends on the packaging of (pre-) genomic RNA and identified two distinct signals within the cis-acting sequences (CASI and CASII), Pol encapsidation sequences (PESI and PESII), which are required for Pol capsid incorporation. Here, we investigated whether the presence of PESI and PESII in an FV vector is sufficient for Pol encapsidation and whether the rather extended CASII element can be shortened without loss of functionality. Our results indicate that (i) the presence of PESI and II are not sufficient for Pol encapsidation, (ii) prototype FV vectors with a shortened CASII element retain Pol incorporation and full functionality, in particular upon transducing fibroblasts and primary human mesenchymal stem cells, (iii) the presence of the central poly purine tract significantly increased the transduction rates of FV vectors and (iv) Pol encapsidation and RNA packaging can be clearly separated. In essence, we designed a new FV vector that bears approximately 850 bp less of CAS than previously established vectors and is fully functional when analysed to transduce cell lines and primary human cells.
Effects of multiple amino acids of the parainfluenza virus 5 fusion protein on its haemagglutinin–neuraminidase-independent fusion activity
Authors: Ito Morihiro , Nishio Machiko , Kawano Mitsuo , Komada Hiroshi , Ito Yasuhiko , Tsurudome Masato
Published: January 2009

The fusion (F) protein of parainfluenza virus 5 (PIV-5) strain W3A is able to induce cell fusion when it is expressed alone in baby hamster kidney cells, whilst the F protein of PIV-5 strain WR induces cell fusion only when co-expressed with the haemagglutinin–neuraminidase (HN) protein. It has been shown previously that when Leu-22 of the WR F protein is replaced with the W3A F counterpart (Pro-22), the resulting mutant L22P exhibits HN-independent fusion activity. Furthermore, previous chimeric analysis between L22P and the F protein of PIV-5 strain T1 has suggested that Glu-132 also contributes to the HN-independent fusion activity of L22P. It was shown here that substitution of Glu-132 of L22P with various amino acids including the T1 F protein counterpart (Lys-132) resulted in a reduction in fusion activity, whereas substitution with Asp was the exception in being tolerated. Interestingly, reduced fusion activity of an L22P mutant that harboured the E132K substitution could be restored by an additional D416K substitution but not by a D416E mutation, suggesting that the presence of the same charge at positions 132 and 416 is important for the HN-independent fusion activity. In contrast, substitution of Leu-22 of the WR F protein with various amino acids except those with aliphatic side chains resulted in acquisition of fusion activity, suggesting that the HN dependence of the WR F protein in the induction of cell fusion is attributable to the hydrophobicity of Leu-22. These results indicate that at least three amino acids are involved in the HN-independent fusion activity of the PIV-5 F protein.
Construction of an infectious cDNA clone of hepatitis E virus strain JE03-1760F that can propagate efficiently in cultured cells
Authors: Yamada Kentaro , Takahashi Masaharu , Hoshino Yu , Takahashi Hideyuki , Ichiyama Koji , Tanaka Toshinori , Okamoto Hiroaki
Published: January 2009

A full-length infectious cDNA clone (pJE03-1760F/wt) of a genotype 3 hepatitis E virus (HEV) (strain JE03-1760F) obtained from a faecal specimen was constructed in this study. Upon transfection of the capped in vitro transcripts of pJE03-1760F/wt into PLC/PRF/5 cells, the viral RNA levels in the culture supernatant started to increase on day 6 post-transfection (p.t.) and reached 107 copies ml−1 on day 28 p.t. Detection of increasing numbers of cells with ORF2 protein expression by immunofluorescence assay at 5, 7, 11 and 15 days p.t. indicated the spread of HEV infection in cell culture. When the cDNA-derived virus in culture supernatant was inoculated into PLC/PRF/5 or A549 cells, it grew as efficiently as the faeces-derived virus in both cells, reaching 106 copies ml−1 at 30 days post-inoculation. Our reverse genetics system for HEV that is usable in a robust cell-culture system will be useful for elucidation of the mechanism of HEV replication and functional roles of HEV proteins.
Is laparoscopic surgery acceptable for advanced colon cancer?
Authors: Kitano Seigo , Inomata Masafumi
Published: January 2009

Laparoscopic surgery is widespread in the treatment of colorectal cancer. In Japan, a nationwide survey has shown that the rate of advanced colorectal cancer has increased gradually to 65% of total laparoscopic surgeries in 2007. Many randomized controlled trials have demonstrated that in the short term, laparoscopic surgery is feasible, safe, and has many benefits, including reduction of peri‐operative mortality. In terms of long‐term outcomes, four randomized controlled trials suggest that there are no differences in laparosupic and open surgery for colon cancer. However, important issues, including long‐term oncological outcome, cost effectiveness, and the impact on the quality of life of patients, should be addressed in well‐designed large‐scale trials. In Japan, a retrospective multicenter study has demonstrated that the short‐term outcomes of laparoscopic surgery are beneficial, and the long‐term outcomes are the same as for open surgery. In 2004, a prospective large‐scale randomized controlled trial (JCOG0404) to compare laparoscopic surgery with open surgery was started to evaluate oncological outcomes for advanced colon cancer. This trial is supported in part by a Grant‐in‐Aid for Cancer Research from the Japanese Ministry of Health, Labour, and Welfare. In the present study, laparoscopic surgery is found to be acceptable for stage I disease of colon cancer, whereas it is controversial for stage II/III disease because of inadequate clinical evidence. Whether laparoscopic surgery is acceptable for advanced colon cancer or not should be confirmed by the Japanese large‐scale prospective randomized controlled trial (JCOG0404) in the near future. (Cancer Sci 2009; 100: 567–571)
Repeated high‐frequency transcranial magnetic stimulation over the dorsolateral prefrontal cortex reduces cigarette craving and consumption
Authors: Amiaz Revital , Levy Dino , Vainiger Dana , Grunhaus Leon , Zangen Abraham
Published: January 2009

Aims  To evaluate the effect of repeated high‐frequency transcranial magnetic stimulation (rTMS) of the left dorsolateral prefrontal cortex (DLPFC), combined with either smoking or neutral cues, on cigarette consumption, dependence and craving.

Design  Participants were divided randomly to real and sham stimulation groups. Each group was subdivided randomly into two subgroups presented with either smoking‐related or neutral pictures just before the daily TMS intervention. Ten daily rTMS sessions were applied every week‐day and then a maintenance phase was conducted in which rTMS sessions were less frequent.

Setting  Single‐site, out‐patient, randomized, double‐blind, sham‐controlled.

Participants  Forty‐eight chronic smokers who smoked at least 20 cigarettes per day and were motivated to quit smoking. Healthy males and females were recruited from the general population using advertisements in newspapers and on internet websites.

Intervention  Ten daily rTMS sessions were administered using a standard figure‐8 coil over the DLPFC. Stimulation included 20 trains/day at 100% of motor threshold. Each train consisted of 50 pulses at 10 Hz with an inter‐train interval of 15 seconds.

Measurements  Cigarette consumption was evaluated objectively by measuring cotinine levels in urine samples and subjectively by participants' self‐reports. Dependence and craving were evaluated by standard questionnaires.

Findings  Ten daily rTMS sessions over the DLPFC reduced cigarette consumption and nicotine dependence. Furthermore, treatment blocked the craving induced by daily presentation of smoking‐related pictures. However, these effects tended to dissipate over time.

Conclusions  Multiple high‐frequency rTMS of the DLPFC can attenuate nicotine craving.
A randomized, placebo‐controlled study of the effects of naproxen, aspirin, celecoxib or clopidogrel on gastroduodenal mucosal healing
Authors: DIKMAN A. , SANYAL S. , VON ALTHANN C. , WHITSON M. , DESAI J. , BODIAN C. , BROOKS A. , BAMJI N. , COHEN L. , MILLER K. , AISENBERG J.
Published: January 2009

Background  Many individuals with gastroduodenal ulcers require on‐going, non‐steroidal anti‐inflammatory drug (NSAID) or anti‐platelet therapy.

Aims  To evaluate the effects of these agents on gastroduodenal mucosal healing.

Methods  Helicobacter pylori‐negative volunteers were randomized to receive naproxen, celecoxib, aspirin, clopidogrel or placebo. Antral and duodenal lesions were created endoscopically with a biopsy forceps. After 7 days of medication dosing, each lesion was scored [from 0 (low) to 8 (high)] using a validated methodology. The primary endpoint was the mean injury score. The secondary endpoint was the percentage of subjects with ≥1 unhealed lesion.

Results  In all, 108 subjects completed the study. Naproxen impaired antral lesion healing more than placebo, clopidogrel, aspirin or celecoxib (mean injury score of 4.3 vs. 3.0, 2.7, 3.2, and 3.2, respectively, P < 0.05). Naproxen impaired duodenal lesion healing more than placebo, clopidogrel or aspirin (mean injury score of 4.0 vs. 2.4, 2.6, and 2.2, respectively, P < 0.05). More subjects taking naproxen than placebo or clopidogrel had ≥1 unhealed antral lesions (72.2% vs. 36.0% and 32.0%, respectively, P < 0.05) and unhealed duodenal lesions (61.1% vs. 16.0% and 28.0%, respectively, P < 0.05).

Conclusions  Naproxen may impair gastroduodenal healing more than aspirin or celecoxib in H. pylori negative subjects. Clopidogrel did not impair mucosal healing.
Review article: pain and chronic pancreatitis
Authors: LIEB II J. G. , FORSMARK C. E.
Published: January 2009

Background  Pain in chronic pancreatitis chronic pancreatitis is a frustrating and challenging symptom for both the patient and clinician. It is the most frequent and most significant symptom. Many patients fail the currently available conservative options and require opiates or endoscopic/surgical therapy.

Aim  To highlight the pathophysiology and management of chronic pancreatitis pain, with an emphasis on recent developments and future directions.

Methods  Expert review, utilizing in addition a comprehensive search of PubMed utilizing the search terms chronic pancreatitis and pain, treatment or management and a manual search of recent conference abstracts for articles describing pain and chronic pancreatitis.

Results  Pancreatic pain is heterogenous in its manifestations and pathophysiology. First‐line medical options include abstinence from alcohol and tobacco, pancreatic enzymes, adjunctive agents, antioxidants, and non‐opiate or low potency opiate analgesics. Failure of these options is not unusual. More potent opiates, neurolysis and endoscopic and surgical options can be considered in selected patients, but this requires appropriate expertise. New and better options are needed. Future options could include new types of pancreatic enzymes, novel antinociceptive agents nerve growth factors, mast cell‐directed therapy, treatments to limit fibrinogenesis and therapies directed at the central component of pain.

Conclusions  Chronic pancreatitis pain remains difficult to treat. An approach utilizing conservative medical therapies is appropriate, with more invasive therapies reserved for failure of this conservative approach. Treatment options will continue to improve with new and novel therapies on the horizon.
Clinical course of hepatitis B virus infection during pregnancy
Authors: NGUYEN G. , GARCIA R. T. , NGUYEN N. , TRINH H. , KEEFFE E. B. , NGUYEN M. H.
Published: January 2009

Background  For women with hepatitis B virus (HBV) infection, little is known about the natural progression of the disease during pregnancy or its impact on pregnancy outcomes.

Objectives  To investigate the natural progression of HBV infection during pregnancy or its impact on pregnancy outcomes.

Methods  In this retrospective cohort study, we reviewed medical records of all patients who were pregnant and presented with HBsAg‐positivity between 2000 and 2008 at a community gastroenterology practice and a university hepatology clinic. Maternal characteristics were analysed according to maternal and perinatal outcomes.

Results  A total of 29 cases with at least 2 measurements of either HBV DNA or alanine aminotransferase (ALT) levels were included. Older age was the only predictor of a trend towards higher risk of an adverse clinical outcome [OR = 1.21 (0.97–1.51), P = 0.089], defined as either a negative foetal outcome (premature delivery, spontaneous abortion), or a negative maternal outcomes (gestational diabetes mellitus, pre‐eclampsia, hepatic flare, liver failure). This trend for age remained even after adjusting for baseline ALT. Baseline serum HBV DNA, ALT, hepatitis B e antigen status, gravida and parity were not significant predictors for adverse clinical outcomes. Four patients developed liver failure.

Conclusions  Maternal and neonatal outcomes are highly variable in this clinic‐based patient cohort. Severe complications due to HBV infection can occur during pregnancy in previously asymptomatic patients. It is unclear how generalizable the results observed in this cohort would be to the general population; therefore, further studies are needed to identify reliable predictors for significant adverse outcomes and until more data are available, pregnant patients with HBV infection should be monitored with periodic serum HBV DNA and ALT levels.
Ondansetron has similar clinical efficacy against both nausea and vomiting
Authors: Jokela R. M. , Cakmakkaya O. S. , Danzeisen O. , Korttila K. T. , Kranke P. , Malhotra A. , Paura A. , Radke O. C. , Sessler D. I. , Soikkeli A. , Roewer N. , Apfel C. C.
Published: January 2009

Ondansetron is widely believed to prevent postoperative vomiting more effectively than nausea. We analysed data from 5161 patients undergoing general anaesthesia who were randomly stratified to receive a combination of six interventions, one of which was 4 mg ondansetron vs placebo. For the purpose of this study a 20% difference in the relative risks for the two outcomes was considered clinically relevant. Nausea was reduced from 38% (969/2585) in the control to 28% (715/2576) in the ondansetron group, corresponding to a relative risk of 0.74, or a relative risk reduction of 26%. Vomiting was reduced from 17% (441/2585) to 11% (293/2576), corresponding to a relative risk of 0.67, or a relative risk reduction of 33%. The relative risks of 0.67 and 0.74 were clinically similar and the difference between them did not reach statistical significance. We thus conclude that ondansetron prevents postoperative nausea and postoperative vomiting equally well.