bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent Outbreaks of Black Rot of Brassicas Caused by Xanthomonas campestris pv. campestris in Southern Mozambique
Authors: Bila J. , Mondjana A. M. , Wulff E. G. , Mortensen C. N.
Published: October 2009

In August and September of 2007, black rot symptoms were observed on seedbed and field plants of Brassica spp. grown in the southern districts of Boane, Mahotas, and Chòkwé in Mozambique. One hundred eighty-two cabbage-growing households were evaluated for the incidence of Xanthomonas campestris pv. campestris. Five Brassica cultivars, Glory F1, Glory of Enkhuizen, Copenhagen Market, Starke (Brassica oleracea pv. capitata L.), and Tronchuda (B. oleracea L. var. costata DC) were grown in the areas for several years. The hybrid Glory F1 was the most popular grown cultivar in the surveyed areas. In the Boane district, the highest incidence of black rot was recorded on Copenhagen Market (70%), Starke (67.9%), and Glory F1 (67.3%). In Chòkwé, Tronchuda (Portuguese kale) was the least affected Brassica crop. Water-soaked lesions starting at the edge of leaves with typical V-shaped necrotic lesions and vein discoloration were the most commonly observed symptoms. When examined with a microscope, cut edges of symptomatic stem and leaf tissues consistently exhibited bacterial streaming. The bacteria were isolated from commercial seed and field-grown plants on semiselective agar media (2). Forty-six X. campestris pv. campestris strains that were gram negative, aerobic, starch positive, nitrate negative, and oxidase negative or weakly positive (3) were further identified on the basis of ELISA (Agdia Inc., Elhart, IN), GN Biolog Microbial Identification System, version 4.2 (Biolog Inc., Hayward, CA), and PCR-specific primers (1). Pathogenicity tests were conducted by pin inoculating two upper leaves of cabbage (cv. Wirosa) in the 2- to 3-leaf stage with bacterial growth from 24-h-old agar cultures (2). Black rot symptoms developed on nearly all inoculated plants within 7 to 14 days. No symptoms were observed on control plants inoculated with a sterile pin without bacterial inoculum. The severity of black rot of Brassica spp. in three important farming districts caused significant losses in Mozambique.

References: (1) T. Berg et al. Plant Pathol. 54:416, 2005. (2) S. J. Roberts and H. Koenraadt. Page 1 in: International Rules for Seed Testing: Annexe to Chapter 7 Seed Health Methods. ISTA, 2007. (3) N. W. Schaad et al. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2001.
First Report of Faba bean necrotic yellows virus Affecting Legume Crops in Azerbaijan
Authors: Kumari S. G. , Attar N. , Mustafayev E. , Akparov Z.
Published: October 2009

A total of 482 chickpea (Cicer arietinum L.), 182 lentil (Lens culinaris Medik.), 12 vetch (Vicia sativa L.), 5 field pea (Pisum sativum L.), and 3 faba bean (Vicia faba L.) samples were collected from plants with symptoms suggestive of a viral infection (leaf rolling, yellowing, and stunting) from the major legume-production areas of Azerbaijan in the 2007 and 2008 growing seasons. All samples were tested by the tissue-blot immunoassay (3) at the Virology Laboratory of ICARDA, Syria using 11 specific legume virus antisera including a monoclonal antibody (2-5H9) (1) for Faba bean necrotic yellows virus (FBNYV). Laboratory tests showed that FBNYV was detected in 73, 61, 11, 3, and 2 samples of chickpea, lentil, vetch, field pea, and faba bean, respectively. Total DNA was extracted from six FBNYV-positive samples (two chickpea, two lentil, and two vetch) and tested by PCR with the following four primer sets (FBNYV, Milk vetch dwarf virus [MDV], Subterranean clover stunt virus [SCSV], and nanovirus DNA-R primers [F103 and R101]) (2). All six Azeri samples as well as the reference nanovirus isolates (SCSV-Australia, MDV-Japan, and FBNYV-Syria) generated amplicons of the expected size (~770 bp) using the nanovirus DNA-R primers (F103 & R101). In addition, Azeri samples and FBNYV-Syria yielded a PCR amplicon of the expected size (666 bp) with the FBNYV primer pair. The MDV- and SCSV-specific primers did not generate amplicons with these six samples. Sequence analysis of the FBNYV amplicons from two isolates (AzL 282-07 from lentil [GenBank Accession No. GQ351600] and AzV 277-07 from vetch [GenBank Accession No. GQ371215]) showed that they were 99% identical with each other. Comparing the sequence of AzL 282-07 with that of other nanoviruses revealed identities of 97% (FBNYV-Spain; DQ830990), 96% (FBNYV-Iran; AM493900), 92% (FBNYV-Syria; Y11408), 92% (FBNYV-Egypt; AJ132183), 78% (MDV; AB044387) and 69% (SCSV-Australia; U16734). FBNYV has been reported to infect food legumes in many countries in West Asia and North Africa and cause economic losses on faba bean in Egypt, Jordan, and Syria. To our knowledge, this is the first record of FBNYV infecting legume crops in Azerbaijan.

References: (1) A. Franz et al. Ann. Appl. Biol. 128:255, 1996. (2) S. G. Kumari et al. Phytopathol. Mediterr. 47:42, 2008. (3) K. M. Makkouk and A. Comeau. Eur. J. Plant Pathol. 100:71, 1994.
First Report of Tobacco mosaic virus in Abutilon theophrasti in China
Authors: Niu Y. B. , Qing L. , Yao M. , Wang D. F. , Liu J. D. , Wang J. S.
Published: October 2009

Velvetleaf (Abutilon theophrasti Medic), a tall, fecund, self-fertile annual plant in the family Malvaceae, is widely grown in China as a fiber crop and for its medicinal properties. In July of 2008, we observed diffuse chlorotic and necrotic spots on the oldest leaves of velvetleaf plants in the field in Shanxi Province. Sap extracts from six symptomatic plants were tested by direct antigen coated ELISA using polyclonal antibodies specific to Potato virus Y (PVY) and monoclonal antibodies specific to Tomato mosaic virus (ToMV), Cucumber mosaic virus (CMV), and Tobacco mosaic virus (TMV). Five of the six samples were negative for ToMV, CMV, and PVY but positive for TMV. Double-stranded RNA extracted from leaves of the five velvetleaf plants was used as template for reverse transcription (RT)-PCR as described by Krajačića et al. (1) and Li et al. (2) with some modifications. One-step RT-PCR was performed using a Quant One Step RT-PCR Kit (TIANGEN BIOTECH CO., LTD., Beijing, China) with sense (5′-CTGTTTAGCCGGTTTGGT-3′), and antisense (5′-TCCCTTTACGGACATCAC-3′) primers (3) designed to specifically amplify a fragment of the movement protein coding region of TMV. The expected 470-bp fragments were amplified from dsRNA from these five plants and the amplicon from each plant was cloned and sequenced (GenBank Accession No. FJ873800). Comparisons of a consensus sequence derived from the five amplicons with the nucleotide sequences available in the NCBI database using BLAST showed 99% identity with TMV from South Korea (GenBank Accession No. AB354955) and Spain (Accession No. AJ308692) and 98% with TMV from China (Accession No. AF165190). The serological, RT-PCR results and sequence data revealed that these velvetleaf plants were infected by TMV. On the basis of the serological analysis and genome sequence comparisons, this isolate was tentatively designated as TMV-Velvetleaf. To our knowledge, this is the first report of TMV in Abutilon theophrasti Medic in China.

References: (1) M. Krajačić et al. J. Chromatogr A. 1144:111, 2007. (2) H. Li et al. Agric. Sci. Chin. 6:86, 2007. (3) Y. B. Niu et al. Chin. Biotechnol. 29:76, 2009.
First Report of Bursaphelenchus doui on Tulip Tree (Liriodendron tulipifera) in Korea
Authors: Han H. , Chung Y.-J. , Shin S.-C.
Published: October 2009

Tulip tree (Liriodendron tulipifera) is one the major tree species in Korean plantations, but it originated from North America. Bursaphelenchus doui was collected from the wood of dead tulip trees located at Wanju in Chonnam Province, Korea. Nematodes were maintained in fungal medium culture (Botrytis cinerae) on potato dextrose agar. B. doui is morphologically close to B. xylophilus, a causative organism of pine wilt disease, and identification to species is difficult. However, B. doui differs from the other species of the xyophilus group by the larger spicule (33.8 to 43.3 μm) (1). For accurate species identification, both morphology and molecular biological methods were applied. Morphological observations showed lip region 3.7 μm high and offset by a constriction, median bulb well developed, esophageal gland overlapping intestine dorsally, vulval flap present, tail terminus with distinct mucro. Males ventrally curved by fixation, spicules pared, and large with small, cucullus, oval-shaped bursa. Measurements of 20 females and 10 males (female; body length = 901.7 ± 60.5 μm, a = 34.3 ± 3.1, b = 10.4 ± 1.5, c = 23.0 ± 2.3, V = 77.1 ± 2.0, stylet length = 14.3 ± 0.4 μm, tail length = 39.5 ± 4.2 μm, length of postuterine sac = 104.6 ± 7.8: male; body length = 790.4 ± 40.6 μm, a = 34.4 ± 2.7, b = 10.8 ± 1.7, c = 22.7 ± 1.3, stylet length = 14.3 ± 0.3 μm, tail length = 34.8 ± 1.9 μm, spicules length = 39.5 ± 4.1 μm) were close to the original description of B. doui by Braasch et al. (1). For molecular diagnosis, DNA was extracted from more than 30 individual nematodes with a DNeasy Kit (Qiagen, Valencia, CA) and the internal transgenic spacers (ITS) 1, 2, and 5.8S regions in rDNA were amplified by PCR (US/PTC-0220; Bio Rad, Hercules, CA). ITS-restriction fragment length polymorphism (RFLP) can discriminate closely related species by using five different restriction enzymes (2). ITS-RFLP patterns obtained with these enzymes were the same as reported by Braasch et al. (1). B. doui previously has been detected in Korean wooden packages imported to China (1). However, most production of Korean wooden packages depends on imported coniferous trees from other countries. Although B. doui has been reported in Japanese red pine (Pinus densiflora) in Japan (3), the natural distribution of B. doui in Korea is unclear. On the basis of morphological and molecular biological information, we identify this nematode as B. doui. To our knowledge, this is the first report of B. doui on tulip tree and in a natural area in Korea.

References: (1) H. Braasch et al. Russ. J. Nematol. 12:19, 2004. (2) W. Burgermeister et al. Russ. J. Nematol. 13:29, 2005. (3) N. Kanzaki et al. Nematology. 10:69, 2008.
Some aspects of the airborne transmission of infection
Authors: Clark Raymond P. , de Calcina-Goff Mervyn L.
Published: October 2009

The relationship between the human body and the dissemination of potentially pathogenic particles and droplets is described. Airborne transmission of infection in operating theatres and a burns unit and the part played by the human microclimate and its interaction with ventilating air flows is discussed. The mechanisms by which different garment assemblies used for surgery can enhance particle dispersion are illustrated and the way that floor cleaning can increase the concentration of airborne organisms is described. The development of the successful use of ultra-clean air systems in orthopaedic implant surgery is reviewed. Relationships between contact and airborne transmission of disease are explored and ways by which containment strategies and metrics used in pharmaceutical and electronics manufacturing can be applied to the design and monitoring of healthcare areas is discussed. It is suggested that currently available techniques involving architectural, ventilation and operational aspects of healthcare provision, when properly applied, can markedly improve treatment outcomes that may otherwise be compromised by hospital-acquired infections involving both bacteria and viruses.
A schlieren optical study of the human cough with and without wearing masks for aerosol infection control
Authors: Tang Julian W. , Liebner Thomas J. , Craven Brent A. , Settles Gary S.
Published: October 2009

Various infectious agents are known to be transmitted naturally via respiratory aerosols produced by infected patients. Such aerosols may be produced during normal activities by breathing, talking, coughing and sneezing. The schlieren optical method, previously applied mostly in engineering and physics, can be effectively used here to visualize airflows around human subjects in such indoor situations, non-intrusively and without the need for either tracer gas or airborne particles. It accomplishes this by rendering visible the optical phase gradients owing to real-time changes in air temperature. In this study, schlieren video records are obtained of human volunteers coughing with and without wearing standard surgical and N95 masks. The object is to characterize the exhaled airflows and evaluate the effect of these commonly used masks on the fluid-dynamic mechanisms that spread infection by coughing. Further, a high-speed schlieren video of a single cough is analysed by a computerized method of tracking individual turbulent eddies, demonstrating the non-intrusive velocimetry of the expelled airflow. Results show that human coughing projects a rapid turbulent jet into the surrounding air, but that wearing a surgical or N95 mask thwarts this natural mechanism of transmitting airborne infection, either by blocking the formation of the jet (N95 mask), or by redirecting it in a less harmful direction (surgical mask).
Movement of airborne contaminants in a hospital isolation room
Authors: Eames I. , Shoaib D. , Klettner C. A. , Taban V.
Published: October 2009

We analyse the characteristics of a force-ventilated isolation room, and the contributions to transport caused by the movement of people and doors opening/closing.

The spread of fine droplets and particles can be understood, to leading order, by considering the movement of passive contaminants. A scaled (1:10) model of an isolation room (with water instead of air) was used to analyse the dilution of a passive contaminant (food dye), released either instantaneously or at a constant rate. The high level of turbulence, typical of isolation rooms, ensures that the dye concentration is uniform within the model room and mixing is perfect, and the measured mean concentration can be predicted theoretically. In a second series of experiments, the exchange generated by a door opening/closing is measured for different opening angles. A dipolar vortex is generated at the tip of the door which moves into the centre of the room, with a large coherent structure moving along the wall. The exchange volume is comparable to the swept volume of the door.

Larger droplets and particles do not move passively. Their movement within a turbulent flow is studied by combining a Lagrangian model of particle movement with a kinematic simulation of a pseudo turbulent flow. The results show that while the mean fall velocity of particles is largely unchanged, turbulence significantly enhances horizontal and vertical dispersion. The horizontal spread as a function of the level of turbulence and droplet properties is estimated.

The conclusions from both studies are brought together and discussed in the context of the airborne spread of contaminants within a general hospital room.
Enzymic colorimetry-based DNA chip: a rapid and accurate assay for detecting mutations for clarithromycin resistance in the 23S rRNA gene of Helicobacter pylori
Authors: Xuan Shi-Hai , Zhou Yu-Gui , Shao Bo , Cui Ya-Lin , Li Jian , Yin Hong-Bo , Song Xiao-Ping , Cong Hui , Jing Feng-Xiang , Jin Qing-Hui , Wang Hui-Min , Zhou Jie
Published: October 2009

Macrolide drugs, such as clarithromycin (CAM), are a key component of many combination therapies used to eradicateHelicobacter pylori. However, resistance to CAM is increasing inH. pyloriand is becoming a serious problem inH. pylorieradication therapy. CAM resistance inH. pyloriis mostly due to point mutations (A2142G/C, A2143G) in the peptidyltransferase-encoding region of the 23S rRNA gene. In this study an enzymic colorimetry-based DNA chip was developed to analyse single-nucleotide polymorphisms of the 23S rRNA gene to determine the prevalence of mutations in CAM-related resistance inH. pylori-positive patients. The results of the colorimetric DNA chip were confirmed by direct DNA sequencing. In 63 samples, the incidence of the A2143G mutation was 17.46 % (11/63). The results of the colorimetric DNA chip were concordant with DNA sequencing in 96.83 % of results (61/63). The colorimetric DNA chip could detect wild-type and mutant signals at every site, even at a DNA concentration of 1.53×102 copies μl−1. Thus, the colorimetric DNA chip is a reliable assay for rapid and accurate detection of mutations in the 23S rRNA gene ofH. pylorithat lead to CAM-related resistance, directly from gastric tissues.
Monomicrobial necrotizing fasciitis in a white male caused by hypermucoviscous Klebsiella pneumoniae
Authors: Gunnarsson Gudjon L. , Brandt Pernille B. , Gad Dorte , Struve Carsten , Justesen Ulrik S.
Published: October 2009

We report a case of monomicrobial necrotizing fasciitis caused by hypermucoviscous Klebsiella pneumoniae in an immunocompromised white male after travel to China. The K. pneumoniae isolate belonged to the K2 serotype, and carried the virulence factors RmpA and aerobactin. To the best of our knowledge this is the first report of necrotizing fasciitis caused by hypermucoviscous K. pneumoniae resembling the highly virulent K. pneumoniae isolates associated with liver abscess syndrome in Asia.
Evaluation of CHROM-Pal medium for the isolation and direct identification of Candida dubliniensis in primary cultures from the oral cavity
Authors: Sahand Ismail H. , Maza José L. , Eraso Elena , Montejo Miguel , Moragues María D. , Aguirre José M. , Quindós Guillermo , Pontón José
Published: October 2009

Candida albicans is the species most frequently isolated from oral specimens, but the recovery of other Candida species such as Candida dubliniensis is increasing. Differentiation of C. dubliniensis from C. albicans requires special tests and both species are misidentified in some studies. CHROM-Pal (CH-P) is a novel chromogenic medium used in our laboratory for differentiation between C. albicans and C. dubliniensis on the basis of colony colour and morphology, and chlamydospore production. The performance of CH-P and CHROMagar Candida (CAC) was compared for primary isolation and presumptive identification of yeasts from oral specimens from human immunodeficiency virus (HIV)-infected and uninfected individuals. The identification of Candida species on both media was compared with two reference identification methods (API ID 32 C and multiplex PCR). A total of 137/205 oral swabs (66.8 %) plated onto CH-P and CAC media were positive by culture and resulted in the growth of 171 isolates of Candida species on CH-P, whilst only 159 isolates grew on CAC. C. albicans was the most frequently isolated species in both groups of patients, followed by Candida parapsilosis in the HIV-negative group, and by C. dubliniensis in the HIV-infected group. The other Candida species isolated were Candida guilliermondii, Candida glabrata, Candida krusei, Candida tropicalis, Candida famata, Candida rugosa, Candida kefyr, Candida pelliculosa and Candida pulcherrima. The sensitivity and specificity for identifying C. albicans, C. krusei, C. tropicalis and C. dubliniensis on CH-P were over 98.5 %, always equal to or higher than those obtained when CAC was used. CH-P is a simple reliable medium for primary isolation and presumptive identification of yeast isolates from oral samples. The ability of CH-P to discriminate between C. dubliniensis and C. albicans was significantly higher (P <0.05) than that of CAC.
Xylitol and capsular gene expression in Streptococcus pneumoniae
Authors: Kurola Paula , Tapiainen Terhi , Kaijalainen Tarja , Uhari Matti , Saukkoriipi Annika
Published: October 2009

Xylitol is a sugar alcohol that inhibits the growth and adherence of Streptococcus pneumoniae. In clinical trials, xylitol has been shown to decrease the occurrence of acute otitis media in day-care children but did not decrease nasopharyngeal carriage of the pneumococci. It has also been shown that xylitol affects the ultrastructure of the pneumococcal capsule. Here, it was hypothesized that xylitol might affect the expression of pneumococcal capsular genes. Capsule gene expression levels were studied in 24 clinical pneumococcal isolates and one ATCC strain (49619) by using a real-time RT-PCR method targeting the mRNA of the second gene of the pneumococcal capsular locus, the cpsB gene. The isolates were exposed to 5 % glucose, 5 % xylitol and control medium (brain heart infusion medium containing 10 % fetal bovine serum) for 2 h. cpsB gene expression levels were measured by using a relative quantification method with calibrator normalization where the 16S rRNA gene of pneumococcus was used as a reference. Exposure to xylitol lowered cpsB gene expression levels significantly compared with those in the control (P=0.035) and glucose (P=0.011) media. This finding supports previous results where exposure to xylitol changed the ultrastructure of the pneumococcal capsule and could explain further the high clinical efficacy of xylitol in preventing otitis media.
Characterization of Shigella sonnei isolates from travel-associated cases in Japan
Authors: Izumiya Hidemasa , Tada Yuki , Ito Kenichiro , Morita-Ishihara Tomoko , Ohnishi Makoto , Terajima Jun , Watanabe Haruo
Published: October 2009

Shigella sonneiinfection in industrialized countries is often associated with foreign travel. A total of 195S. sonneiisolates in Japan, isolated from cases associated with foreign travel, were analysed by biotyping and molecular typing using PFGE and multilocus variable-number tandem-repeat analysis (MLVA); their antimicrobial susceptibilities were also evaluated. The isolates were from 26 countries, most of which were Asian. Molecular typing revealed a correlation among the genotypes, biotypes and their geographical areas of origin. The isolates were classified into two biotypes, a and g. Biotype g isolates (n=178) were further divided into distinct clusters mainly on the basis of their geographical areas of origin by both PFGE and MLVA. Isolates from South Asian countries constituted one of the distinct clusters. Biotype g isolates from countries other than South Asia constituted other distinct clusters. Most of the isolates from other countries and continents, excluding the South Asian countries, were included in one major cluster by PFGE analysis. However, by MLVA, they were further divided into minor subclusters mainly on the basis of their countries of origin. MLVA was also demonstrated to be useful in molecular epidemiological analysis, even when only seven loci were applied, resulting in a high resolution with Simpson's index of diversity (D) of 0.993. A core drug-resistance pattern of streptomycin, sulfisoxazole, tetracycline and trimethoprim–sulfamethoxazole was observed in 108 isolates, irrespective of their geographical areas of origin, but the frequency of resistance to nalidixic acid was high among the South Asian and East Asian isolates. Two isolates from China and India were resistant to cefotaxime and harboured theblaCTX-M-14andblaCTX-M-15genes, respectively; these isolates were also resistant to nalidixic acid, which is a matter of concern in terms of shigellosis treatment. Use of a combination of methods was found to be effective for epidemiological investigation in the case ofS. sonneiinfection.
Outbreak of carbapenem-resistant Acinetobacter baumannii carrying the carbapenemase OXA-23 in a German university medical centre
Authors: Kohlenberg Anke , Brümmer Sophie , Higgins Paul G. , Sohr Dorit , Piening Brar C. , de Grahl Clemens , Halle Elke , Rüden Henning , Seifert Harald
Published: October 2009

A prolonged outbreak of carbapenem-resistant Acinetobacter baumannii in a German university medical centre in 2006 was investigated; the investigation included a descriptive epidemiological analysis, a case–control study, environmental sampling, molecular typing of A. baumannii isolates using PFGE and repetitive-sequence-based PCR (rep-PCR) typing, and detection of OXA-type carbapenemases by multiplex PCR. Thirty-two patients acquired the outbreak strain in five intensive care units (ICUs) and two regular wards at a tertiary care hospital within 10 months. The outbreak strain was resistant to penicillins, cephalosporins, ciprofloxacin, gentamicin, tobramycin, imipenem and meropenem, and carried the bla
OXA-23-like gene. Based on PFGE and rep-PCR typing, it was shown to be related to the pan-European A. baumannii clone II. The most likely mode of transmission was cross-transmission from colonized or infected patients via the hands of health-care workers, with the severity of disease and intensity of care (therapeutic intervention scoring system 28 score >median) being independently associated with acquisition of the outbreak strain (odds ratio 6.67, 95 % confidence interval 1.55–36.56). Control of the outbreak was achieved by enforcement of standard precautions, education of personnel, screening of ICU patients for carbapenem-resistant A. baumannii and cohorting of patients. This is believed to be the first report of an outbreak of A. baumannii carrying the carbapenemase OXA-23 in Germany.
Genetic and functional characterization of human immunodeficiency virus type 1 VprC variants from north India: presence of unique recombinants with mosaic genomes from B, C and D subtypes within the open reading frame of Vpr
Authors: Bano Aalia S. , Sood Vikas , Neogi Ujjwal , Goel Nidhi , Kuttiat Vijesh Sreedhar , Wanchu Ajay , Banerjea Akhil C.
Published: October 2009

The human immunodeficiency virus type 1 (HIV-1) epidemic in India is predominantly caused by genetic subtype C, though other minor subtypes have also been reported. One of the major accessory proteins of HIV-1, namely Vpr, is known to influence key steps in viral replication, cell cycle progression, promoter activation, apoptosis and pathogenesis. Therefore, we carried out a genetic and functional analysis of the Vpr variants from eight HIV-1-infected individuals from north India. The sequence analyses revealed that six of eight samples clustered with ancestral subtype C. Remarkably, five of these showed a conserved and region-specific L64P mutation, located in the predicted third α-helix. This change adversely affected their ability to activate the HIV-1 long terminal repeat promoter without compromising their ability to cause apoptosis. Bootscan, phylogenetic and SimPlot analysis of the remaining two samples (VprS2 and A6) revealed very interesting mosaic genomes derived from B, C and D subtypes. The N-terminal half of the VprS2 gene consisted of genomic segments derived from subtypes B/D, C and D but the C-terminal half was derived predominantly from subtype C. Interestingly the N-terminal half of sample A6 also showed similar B/D, C and D inter-subtype recombinant structure but the C-terminal half was entirely derived from the consensus B subtype. Multiple breakpoints in a short stretch of 291 nt encoding the Vpr gene strongly suggest that this region is a potential hot-spot for the formation of inter-subtype recombinants and also highlight the importance of the rapidly evolving HIV-1 epidemic in the north Indian region due to multiple genetic subtypes.
Prion adsorption to stainless steel is promoted by nickel and molybdenum
Authors: Luhr Katarina M. , Löw Peter , Taraboulos Albert , Bergman Tomas , Kristensson Krister
Published: October 2009

Prions are infectious agents resulting from the conversion of a normal cellular protein, PrPC, to a misfolded species, PrPSc. Iatrogenic transmission of prions is known from surgical procedures involving stainless steel materials. Here, it was shown that stainless steel containing nickel and molybdenum binds PrPSc more efficiently and transmits infection to cells in culture to a higher degree than if these elements are not present. Furthermore, both nickel and molybdenum alone adsorbed PrPSc, and nickel powder could be used to extract PrPSc from dilute solutions, thus providing a simple approach to concentration of PrPSc. The fact that nickel and molybdenum in steel alloys increased the binding affinity, and bound infectivity, of PrPSc is an important issue to consider in the manufacture of surgical instruments and abattoir tools.
Characterization of a new genotype and serotype of infectious bronchitis virus in Western Africa
Authors: Ducatez Mariette F. , Martin Ana Moreno , Owoade Ademola A. , Olatoye Isaac O. , Alkali Bello R. , Maikano Issoufou , Snoeck Chantal J. , Sausy Aurelie , Cordioli Paolo , Muller Claude P.
Published: October 2009

Between 2002 and 2007, more than 1000 chickens from commercial farms, live bird markets and backyard farms in Nigeria and Niger were tested for the presence of the infectious bronchitis virus (IBV) genome. Phylogenetic analysis of full-length sequences of the spike 1 (S1) gene revealed a new genotype of IBV that we refer to as ‘IBADAN’. The minimum genetic distance to the closest ‘non-IBADAN’ strains (UK/7/93 at the nucleotide level; H120 and M41 at the amino acid level) reached 24 and 32 % at the nucleotide and amino acid levels, respectively. The full genome of the IBADAN reference strain (NGA/A116E7/2006) had a genetic distance of 9.7–16.4 % at the nucleotide level with all available fully sequenced strains. As IBV S1 plays a major role in antigenicity, the antigenic relatedness of NGA/A116E7/2006 was compared with strains of other serotypes. NGA/A116E7/2006 did not cross-react with antisera against IT02, M41, D274, Connecticut or 793/B strains in virus neutralization assays. NGA/A116E7/2006 cross-reacted with the QX-like strain ITA/90254/2005 but only to a low level (antigenic relatedness of 33 %), suggesting that IBADAN also represents a new serotype. A comparison of S1 sequences identified several amino acids that may play a role in IBV antigenicity. Despite the absence of obvious clinical signs in poultry infected by IBADAN strains, it is important to test the cross-protection of current vaccine strains.
Human immunodeficiency virus type 1 (HIV-1) protease inhibitors block cell-to-cell HIV-1 endocytosis in dendritic cells
Authors: Muratori Claudia , Ruggiero Eliana , Sistigu Antonella , Bona Roberta , Federico Maurizio
Published: October 2009

Sexual transmission is now the most frequent means of diffusion of human immunodeficiency virus type 1 (HIV-1). Even if the underlying mechanism is still largely unknown, there is a consensus regarding the key role played by mucosal dendritic cells (DCs) in capturing HIV through contact with infected subepithelial lymphocytes, and their capacity to spread HIV by trans-infection. We found that HIV protease inhibitors (PIs) reduced virion endocytosis strongly in monocyte-derived immature (i) DCs contacting HIV-1-infected cells, and that this phenomenon led to dramatically impaired trans-infection activity. This inhibitory effect was not mediated by the block of viral protease activity, as it was also operative when donor cells were infected with a PI-resistant HIV-1 strain. The block of virus maturation imposed by PIs did not correlate with significant variations in the levels of virus expression in donor cells or of Gag/Env virion incorporation. Also, PIs did not affect the endocytosis activity of DCs. In contrast, we noticed that PI treatment inhibited the formation of cell–cell conjugates whilst reducing the expression of ICAM-1 in target iDCs. Our results contribute to a better delineation of the mechanisms underlying HIV-1 trans-infection activity in DCs, whilst having implications for the development of new anti-HIV microbicide strategies.
Microarray-based determination of the lytic cascade of human herpesvirus 6B
Authors: Tsao Edward H. , Kellam Paul , Sin Cheryl S. Y. , Rasaiyaah Jane , Griffiths Paul D. , Clark Duncan A.
Published: October 2009

The lytic gene expression of several members of the human herpesvirus family has been profiled by using gene-expression microarrays; however, the lytic cascade of roseoloviruses has not been studied in similar depth. Based on the complete DNA genome sequences of human herpesvirus 6 variant A (HHV-6A) and variant B (HHV-6B), we constructed a cDNA microarray containing DNA probes to their predicted open reading frames, plus 914 human genes. Gene-expression profiling of HHV-6B strain Z29 in SupT1 cells over a 60 h time-course post-infection, together with kinetic classification of the HHV-6B genes in the presence of either cycloheximide or phosphonoacetic acid, allowed the placement of HHV-6B genes into defined kinetic classes. Eighty-nine HHV-6B genes were divided into four different expression kinetic classes: eight immediate-early, 44 early, 33 late and four biphasic. Clustering of genes with similar expression profiles implied a shared function, thus revealing possible roles of previously uncharacterized HHV-6B genes.
Detection and quantification of human bocavirus in river water
Authors: Hamza Ibrahim Ahmed , Jurzik Lars , Wilhelm Michael , Überla Klaus
Published: October 2009

Human bocavirus (HBoV) was recently discovered in children with respiratory-tract infection and has been detected frequently in faecal specimens from children with gastroenteritis. The present study addresses for the first time, to our knowledge, the prevalence of HBoV in river water. By using a newly developed real-time PCR targeting a conserved region of the NP1 gene of HBoV, virus levels in water samples were determined. Moreover, partial sequence analysis of the NP1 gene of HBoV and comparative phylogenetic analysis were performed. HBoV was detected in 40.8 % of collected water samples. The virus level ranged between 3×101 and 2×103 genome equivalents l−1. Therefore, the present study suggests that river water could play a role in the spread of HBoV. However, further work should be done to determine the actual risk of infection via surface water.
Mumps virus Enders strain is sensitive to interferon (IFN) despite encoding a functional IFN antagonist
Authors: Young D. F. , Galiano M. C. , Lemon K. , Chen Y.-H. , Andrejeva J. , Duprex W. P. , Rima B. K. , Randall R. E.
Published: October 2009

Although the Enders strain of mumps virus (MuV) encodes a functional V protein that acts as an interferon (IFN) antagonist, in multi-cycle growth assays MuV Enders grew poorly in naïve (‘IFN-competent’ Hep2) cells but grew to high titres in ‘IFN-compromised’ Hep2 cells. Even so, the growth rate of MuV Enders was significantly slower in ‘IFN-compromised’ Hep2 cells when compared with its replication rate in Vero cells and with the replication rate of parainfluenza virus type 5 (a closely related paramyxovirus) in both naïve and ‘IFN-compromised’ Hep2 cells. This suggests that a consequence of slower growth is that the IFN system of naïve Hep2 cells can respond quickly enough to control the growth of MuV Enders. This is supported by the finding that rapidly growing variants of MuV Enders that were selected on ‘IFN-compromised’ Hep2 cells (i.e. in the absence of any selection pressure exerted by the IFN response) also grew to high titres on naïve Hep2 cells. Sequencing of the complete genome of one of these variants identified a single point mutation that resulted in a substitution of a conserved asparagine by histidine at position 498 of the haemagglutinin–neuraminidase protein, although this mutation was not present in all rapidly growing variants. These results support the concept that there is a race between the ability of a cell to detect and respond to virus infection and the ability of a virus to block the IFN response. Importantly, this emphasizes that factors other than viral IFN antagonists influence the sensitivity of viruses to IFN.
Analysis of recombination between viral RNAs and transgene mRNA under conditions of high selection pressure in favour of recombinants
Authors: Morroni Marco , Thompson Jeremy R. , Tepfer Mark
Published: October 2009

One possible environmental risk related to the utilization of virus-resistant transgenic plants expressing viral sequences is the emergence of new viruses generated by recombination between the viral transgene mRNA and the RNA of an infecting virus. This hypothesis has been tested recently for cucumber mosaic virus (CMV) by comparing the recombinant populations in transgenic and non-transgenic plants under conditions of minimal selection pressure in favour of the recombinants. Equivalent populations were observed in transgenic and non-transgenic plants but, in both, there was a strongly dominant hotspot recombinant which was shown recently to be nonviable alone in planta, suggesting that its predominance could be reduced by applying an increased selection pressure in favour of viable recombinants. Partially disabled I17F-CMV mutants were created by engineering 6 nt deletions in five sites in the RNA3 3′-non-coding region (3′-NCR). One mutant was used to inoculate transgenic tobacco plants expressing the coat protein and 3′-NCR of R-CMV. A total of 22 different recombinant types were identified, of which 12 were, as expected, between the transgene mRNA and the mutated I17F-CMV RNA3, while 10 resulted from recombination between the mutated RNA3 and I17F-CMV RNA1. Twenty recombinants were of the aberrant type, while two, including the dominant one detected previously under conditions of minimal selection pressure, were homologous recombinants. All recombinants detected were very similar to ones observed in nature, suggesting that the deployment of transgenic lines similar to the one studied here would not lead to the emergence of new viruses.
Adeno-associated virus serotype 2 induces cell-mediated immune responses directed against multiple epitopes of the capsid protein VP1
Authors: Madsen Declan , Cantwell Emma R. , O'Brien Timothy , Johnson Patricia A. , Mahon Bernard P.
Published: October 2009

Adeno-associated virus serotype 2 (AAV-2) has been developed as a gene therapy vector. Antibody and cell-mediated immune responses to AAV-2 or AAV-2-transfected cells may confound the therapeutic use of such vectors in clinical practice. In one of the most detailed examinations of AAV-2 immunity in humans to date, cell-mediated and humoral immune responses to AAV-2 were characterized from a panel of healthy blood donors. The extent of AAV-2-specific antibody in humans was determined by examination of circulating AAV-2-specific total IgG levels in plasma from 45 normal donors. Forty-one donors were seropositive and responses were dominated by IgG1 and IgG2 subclasses. Conversely, AAV-2-specific IgG3 levels were consistently low in all donors. Cell-mediated immune recall responses were detectable in nearly half the population studied.In vitrorestimulation with AAV-2 of peripheral blood mononuclear cell cultures from 16 donors elicited gamma interferon (IFN-γ) (ten donors), interleukin-10 (IL-10) (eight donors) and interleukin-13 (IL-13) (four donors) responses. Using a series of overlapping peptides derived from the sequence of the VP1 viral capsid protein, a total of 59 candidate T-cell epitopes were identified. Human leukocyte antigen characterization of donors revealed that the population studied included diverse haplotypes, but that at least 17 epitopes were recognized by multiple donors and could be regarded as immunodominant. These data indicate that robust immunological memory to AAV-2 is established. The diversity of sequences recognized suggests that attempts to modify the AAV-2 capsid, as a strategy to avoid confounding immunity, will not be feasible.
Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda
Authors: Cook Shelley , Moureau Gregory , Harbach Ralph E. , Mukwaya Louis , Goodger Kim , Ssenfuka Fred , Gould Ernest , Holmes Edward C. , de Lamballerie Xavier
Published: October 2009

The genus Flavivirus, which contains approximately 70 single-stranded, positive-sense RNA viruses, represents a unique model for studying the evolution of vector-borne disease, as it includes viruses that are mosquito-borne, tick-borne or have no known vector. Both theoretical work and field studies suggest the existence of a large number of undiscovered flaviviruses. Recently, the first isolation of cell fusing agent virus (CFAV) was reported from a natural mosquito population in Puerto Rico, and sequences related to CFAV have been discovered in mosquitoes from Thailand. CFAV had previously been isolated from a mosquito cell line in 1975 and represented the only known ‘insect-only’ flavivirus, appearing to replicate in insect cells alone. A second member of the ‘insect-only’ group, Kamiti River virus (KRV), was isolated from Kenyan mosquitoes in 2003. A third tentative member of the ‘insect-only’ group, Culex flavivirus (CxFV), was first isolated in 2007 from Japan and further strains have subsequently been reported from the Americas. We report the discovery, isolation and characterization of two novel ‘insect-only’ flaviviruses from Entebbe, Uganda: a novel lineage tentatively designated Nakiwogo virus (NAKV) and a new strain of CxFV. The individual mosquitoes from which these strains were isolated, identified retrospectively by using a reference molecular phylogeny generated using voucher specimens from the region, were Mansonia africana nigerrima and Culex quinquefasciatus, respectively. This represents the first isolation, to our knowledge, of a novel insect-only flavivirus from a Mansonia species and the first isolation of a strain of CxFV from Africa.
The NIH Human Microbiome Project
Authors:   The NIH HMP Working Group, Peterson Jane , Garges Susan , Giovanni Maria , McInnes Pamela , Wang Lu , Schloss Jeffery A. , Bonazzi Vivien , McEwen Jean E. , Wetterstrand Kris A. , Deal Carolyn , Baker Carl C. , Di Francesco Valentina , Howcroft T. Kevin , Karp Robert W. , Lunsford R. Dwayne , Wellington Christopher R. , Belachew Tsegahiwot , Wright Michael , Giblin Christina , David Hagit , Mills Melody , Salomon Rachelle , Mullins Christopher , Akolkar Beena , Begg Lisa , Davis Cindy , Grandison Lindsey , Humble Michael , Khalsa Jag , Little A. Roger , Peavy Hannah , Pontzer Carol , Portnoy Matthew , Sayre Michael H. , Starke-Reed Pamela , Zakhari Samir , Read Jennifer , Watson Bracie , Guyer Mark
Published: October 2009

The Human Microbiome Project (HMP), funded as an initiative of the NIH Roadmap for Biomedical Research (http://nihroadmap.nih.gov), is a multi-component community resource. The goals of the HMP are: (1) to take advantage of new, high-throughput technologies to characterize the human microbiome more fully by studying samples from multiple body sites from each of at least 250 “normal” volunteers; (2) to determine whether there are associations between changes in the microbiome and health/disease by studying several different medical conditions; and (3) to provide both a standardized data resource and new technological approaches to enable such studies to be undertaken broadly in the scientific community. The ethical, legal, and social implications of such research are being systematically studied as well. The ultimate objective of the HMP is to demonstrate that there are opportunities to improve human health through monitoring or manipulation of the human microbiome. The history and implementation of this new program are described here.
If cannabis caused schizophrenia—how many cannabis users may need to be prevented in order to prevent one case of schizophrenia? England and Wales calculations
Authors: Hickman Matt , Vickerman Peter , Macleod John , Lewis Glyn , Zammit Stan , Kirkbride James , Jones Peter
Published: October 2009

Background  We consider how many cannabis users may need to be prevented in order to prevent one case of schizophrenia or psychosis [defined as number needed to prevent (NNP)].

Method  Calculation for England and Wales using best available estimates of: incidence of schizophrenia; rates of heavy and light cannabis use; and risk that cannabis causes schizophrenia.

Results  In men the annual mean NNP for heavy cannabis and schizophrenia ranged from 2800 [90% confidence interval (CI) 2018–4530] in those aged 20–24 years to 4700 (90% CI 3114–8416) in those aged 35–39. In women, mean NNP for heavy cannabis use and schizophrenia ranged from 5470 (90% CI 3640–9839) in those aged 25–29 to 10 870 (90% CI 6786–22 732) in 35–39‐year‐olds. Equivalent mean NNP for heavy cannabis use and psychosis were lower, from 1360 (90% CI 1007–2124) in men aged 20–24 and 2480 (90% CI 1408–3518) in women aged 16–19. The mean and median number of light cannabis users that would need to be prevented in order to prevent one case of schizophrenia or psychosis per year are four to five times greater than among heavy users.

Conclusions  The number of young people who need to be exposed to an intervention to generate NNP and prevent one case of schizophrenia will be even larger. The public health importance of preventing cannabis to reduce schizophrenia or psychosis remains uncertain. More attention should be given to testing the hypothesis that cannabis is related causally to psychotic outcomes, and to considering what strategies will be the most effective in reducing heavy cannabis use among young people.
Prolonged myoclonus after a single bolus dose of propofol
Authors: Tam M. K. P. , Irwin M. G. , Tse M. L. , Lui Y. W. A. , Law K. I. , Ng P. W.
Published: October 2009

Propofol is a commonly used anaesthetic agent and is rarely associated with seizure‐like phenomena. This case report presents a young woman with seizure‐like phenomena lasting more than 4 weeks after a single dose of propofol. The underlying pathophysiology of this condition is poorly understood but a psychological component is possible in this case.
Assessing the clinical or pharmaco‐economical benefit of target controlled desflurane delivery in surgical patients using the Zeus® anaesthesia machine*
Authors: Lortat‐Jacob B. , Billard V. , Buschke W. , Servin F.
Published: October 2009

The Zeus® anaesthesia machine includes an auto‐control mode which allows targeting of end‐tidal volatile and inspired oxygen concentrations. We assessed the clinical benefits and economic impact of this target‐controlled anaesthesia compared with conventional manually controlled anaesthesia. Eighty patients were randomly assigned to receive desflurane either with a fresh gas flow set by the anaesthetist or in auto‐control mode. Drug delivery was adjusted to maintain bispectral index between 40–60 units and systolic arterial pressure under 15 mmHg above its pre‐induction value (upper limit) and over 90 mmHg (lower limit). Blood pressure was maintained in the desired range for 89% and 91% of the maintenance period for auto‐control and manual control respectively (p = 0.49). Bispectral index was in the desired range for 82% and 79% of the maintenance period, for auto‐control and manual control respectively (p = 0.46). Oxygen consumption was more than halved by the use of auto‐control mode, and mean (SD) desflurane consumption during surgery was 0.07 (0.04) vs 0.2 (0.07) ml.min−1 in auto‐control and manual control respectively (p < 0.0001). The number of drug delivery adjustments per hour was significantly lower in auto‐control mode (mean (SD) 7 (2) vs 15 (12); p < 0.0001). Thus, the auto‐control mode provided similar haemodynamic stability and bispectral control as did conventional manually controlled anaesthesia, but led to a reduction in gas and vapour consumption with a more clinically acceptable workload.