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J Stanley

Publications and source records attributed to J Stanley.

At least 19 recordsLinked to original sources
PubMed2006

Subviral agents associated with plant single-stranded DNA viruses.

Begomoviruses (family Geminiviridae) are responsible for many economically important crop diseases worldwide. The majority of these diseases are caused by bipartite begomovirus infections, although a rapidly growing number of diseases of the Old World are associated with monopartite begomoviruses. With the exception of several diseases of tomato, most of these are caused by a monopartite begomovirus in association with a recently discovered essential satellite component (DNA-beta). These begomovirus/satellite disease complexes are widespread and diverse and collectively infect a wide variety of crops, weeds and ornamental plants. Non-essential subviral components (DNA-1) originating from nanoviruses are frequently associated with these disease complexes, and there are tantalizing hints that further novel satellites may also be associated with some begomovirus diseases. DNA-beta components can be maintained in permissive plants by more than one distinct begomovirus, reflecting less stringent requirements for trans-replication that will undoubtedly encourage diversification and adaptation as a consequence of component exchange and recombination. In view of their impact on agriculture, there is a pressing need to develop a more comprehensive picture of the diversity and distribution of the disease complexes. A greater understanding of how they elicit the host response may provide useful information for their control as well as an insight into plant developmental processes.

Agriculture↗
PubMed2005

Performing hand actions assists the visual discrimination of similar hand postures.

Recent theoretical work has suggested that internal predictive signals are used for motor control and coordination. The predictive signal - proposed to be the output of a forward model - would be a sensory representation of action. Hence, these sensory representations could potentially influence other sensory processes. We report here how performance of hand actions assisted the visual discrimination of target hand postures presented at random times within an on-going series of hand images. Reaction times to discriminate the targets were significantly shorter when the displayed images were both sequential and congruent with the action being performed. Hence, the planning or execution of action appears to allow better prediction of a displayed series of congruent images. In further control experiments, we show that the motor-visual priming effect is unlikely to be due to differential attentional demands and it is specific to a first person perspective display; it is short lasting, being lost if a 500 ms delay is introduced between successive stimulus presentations. The data are interpreted as evidence supporting the hypothesis that forward models in the motor system provide action-specific sensory predictions that are available to cognitive processes.

Adolescent↗
PubMed2005

Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors.

Geminivirus taxonomy and nomenclature is increasing in complexity with time, and the growing number of geminivirus sequences deposited in gene banks requires regular taxonomic updates and calls for new descriptors to identify virus isolates unambiguously. Fauquet et al. [1] proposed a system to standardize the names of the viruses, and corresponding guidelines have been followed since, rendering nomenclature much easier. Recently, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% identity threshold between complete DNA-A component nucleotide sequences of begomoviruses. This threshold has been utilised since with general satisfaction. In this paper, we review the status of geminivirus species demarcation and nomenclature for a total of 389 isolates. A small number of corrections have been made to comply with the adopted demarcation criteria but otherwise the classification system has remained robust and therefore we propose to continue using it. However, the large numbers of geminivirus sequences that have become available have led us to recognize the need for a better description of virus isolates. The pairwise comparison distribution below the taxonomic level of species identified two peaks, one at 90-91% identity that may correspond to "strains" and one at 96-98% identity that may correspond to "variants". Guidelines for descriptors for each of these levels are proposed to standardize nomenclature. As a consequence, we have revisited the status of some virus isolates to elevate them to "strains". An updated list of all geminivirus isolates currently available is provided.

DNA, Viral↗
PubMed2005

Biolistic infection of cassava using cloned components of Indian cassava mosaic virus.

Cassava mosaic disease (CMD) is a major constraint to cassava production in Africa and Asia. Of the two begomoviruses associated with CMD on the Indian subcontinent, Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus, only the latter has been successfully reintroduced into cassava to resolve the aetiology of the disease. Here, we report the complete nucleotide sequence of an ICMV isolate from Maharashtra (ICMV-[Mah2]), central India. Biolistic inoculation of the cloned components produced a systemic infection and typical mosaic symptoms in cassava, thereby fulfilling Koch's postulates. The availability of infectious clones will provide a valuable tool to screen new cassava cultivars for disease resistance under defined conditions.

DNA, Viral↗
PubMed2005

Experience of hepatitis C among current or former heroin users attending general practice.

The majority of injecting drug users in Ireland are infected with hepatitis C (HCV) and many attend general practice for methadone maintenance treatment. To describe awareness and experience of HCV infection, related investigations and treatment, a semi-qualitative interview study of current or former heroin users attending a general practice was carried out. Twenty-five patients (69% of total) were interviewed, of whom 23 were on methadone maintenance therapy at the time of the interview and 22 were HCV positive. While awareness of harm reduction measures and health implications of the infection was good, continued high-risk activity was common. Negative experiences at diagnosis, of subsequent investigations and treatments received were common. Only one person had been treated for HCV. We conclude there are a number of barriers to effective HCV management among heroin users and further research is needed to improve our understanding of this issue.

Adolescent↗
PubMed2004

Diversity of begomovirus DNA beta satellites of non-malvaceous plants in east and south east Asia.

Two previous analyses of the diversity of begomovirus-associated DNA beta satellites focused predominantly on molecules originating from the Indian sub-continent and southern China. They showed the satellites to group according to the hosts from which they were isolated, either malvaceous or non-malvaceous plants, and then to form sub-groups based upon geographic origin and host. In this study we analysed the diversity of DNA beta satellites in east and south east Asia. Here the satellites group by geographic location and are considerably more diverse than previously indicated. This probably reflects the limited movement of begomovirus/DNA beta complexes in this region and their subsequent diversification from a common ancestor to a variety of hosts.

Asia, Southeastern↗
PubMed2003

Peptide mimotopes as prototypic templates of broad-spectrum surrogates of carbohydrate antigens.

Peptide mimetics of carbohydrate antigens can function as templates to exploit immune mechanisms to augment vaccine design strategies as they are T cell dependent antigens. In this study we evaluate a peptide mimetic (peptide 105) of the Pneumococcal capsular polysaccharide type 14 (Pn14) as a model antigen to explore differences in antigenicity and immunogenicity of peptide mimotopes. The multiple antigenic peptide (MAP) form, by ELISA, competes with native Pn14 in a concentration-dependent manner for binding to an anti-Pn14 monoclonal antibody. It was observed that peptide priming with a conjugated form (105-BSA) and boosting with Pn14 produced higher levels of Pn14-reactive IgG1, IgG2a, IgG2b and IgG3 than priming and boosting with Pn14. This serum also displayed reactivity with multiple serotypes, as assessed by ELISA. However, when compared with serum from humans immunized with the 23-valent pneumococcal vaccines, mimetic-induced mouse serum did not display a significant ability to mediate opsonophagocytic killing of pneumococci. These results suggest the feasibility of designing mimotopes to render effective humoral responses not only to a single serotype of Streptococcus pneumoniae, but to multiple serotypes at once. Such peptides would simplify currently available vaccine approaches, yet highlights the requirement of more extensive polymerization to fully emulate native antigen.

Antibodies, Monoclonal↗
PubMed2002

Detection of campylobacter species: a comparison of culture and polymerase chain reaction based methods.

AIMS: To investigate the optimal method for the detection of campylobacters from stool samples by comparing selective culture with membrane filtration and the polymerase chain reaction (PCR). METHODS: Three hundred and forty three stool samples were investigated by each of the three methods mentioned above. Selective culture was performed with charcoal cefoperazone desoxycholate agar plates. Membrane filtration was performed using cellulose triacetate membranes with 0.45 micro m pores placed on blood agar plates. Enteropathogenic campylobacters were detected using a PCR identification algorithm, consisting of screening PCRs and species identification using a PCR enzyme linked immunosorbent assay (PCR-ELISA), both based on the 16S rRNA gene. RESULTS: Of the 343 samples tested, 23 were positive by one or more method. Of these, 17 were positive by selective culture, 12 by membrane filtration, and 20 by the PCR identification algorithm. A total of 18 of 23 positives were identified as C jejuni and/or C coli by the PCR identification algorithm, compared with 14 identified to the genus level by selective culture, and 10 by membrane filtration. Among the remaining five positive samples, one C hyointestinalis was detected only by the PCR identification algorithm; one C upsaliensis was detected only by the PCR identification algorithm; one Campylobacter sp was detected by membrane filtration and selective culture and later identified as C concisus; one Campylobacter sp was detected by membrane filtration alone and later identified as Arcobacter sp; and one Campylobacter sp detected only by selective culture was lost to study and therefore not speciated. There was no significant difference between detection by selective culture and the other two methods. However, detection by PCR was significantly better than by membrane filtration (0.05 > p > 0.02). CONCLUSION: The PCR identification algorithm can detect and identify Campylobacter spp to the species level and the result is obtained on the same day. However, PCR is expensive, labour intensive, and does not provide an isolate for further identification or typing. Selective culture is as good as the PCR identification algorithm for the detection of the two most common species, C jejuni and C coli, and it is cheap and practical. However, it does miss the less common species, results take 48 hours, and identification is only to the genus level. Membrane filtration showed a low sensitivity compared with the other methods and is not appropriate for the diagnostic laboratory, although it was the only method to detect the Arcobacter sp. The optimum method for the detection of campylobacters from stool samples in the diagnostic laboratory remains selective culture.

Agar↗
PubMed2001

Identification of dna components required for induction of cotton leaf curl disease.

Cotton leaf curl disease (CLCuD) is a major constraint to cotton production in Pakistan. Infectious clones of the monopartite begomovirus cotton leaf curl virus (CLCuV), associated with diseased cotton, are unable to induce typical symptoms in host plants. We have identified and isolated a single-stranded DNA molecule approximately 1350 nucleotides in length which, when coinoculated with the begomovirus to cotton, induces symptoms typical of CLCuD, including vein swelling, vein darkening, leaf curling, and enations. This molecule (termed DNA beta) requires the begomovirus for replication and encapsidation. The CLCuV/DNA 1/DNA beta complex, together with a similar complex previously identified in Ageratum conyzoides, represent members of an entirely new type of infectious, disease-causing agents. The implications of this finding to our understanding of the evolution of new disease-causing agents are discussed.

Base Sequence↗
PubMed2001

Intake of dioxins and related compounds from food in the U.S. population.

The first U.S. nationwide food sampling with measurement of dioxins, dibenzofurans, and coplanar, mono-ortho and di-ortho polychlorinated biphenyls (PCBs) is reported in this study. Twelve separate analyses were conducted on 110 food samples divided into pooled lots by category. The samples were purchased in 1995 in supermarkets in Atlanta, GA, Binghamton, NY, Chicago, IL, Louisville, KY, and San Diego, CA. Human milk also was collected to estimate nursing infants' consumption. The food category with highest World Health Organization (WHO) dioxin toxic equivalent (TEQ) concentration was farm-grown freshwater fish fillet with 1.7 pg/g, or parts per trillion (ppt), wet, or whole, weight. The category with the lowest TEQ level was a simulated vegandiet, with 0.09 ppt. TEQ concentrations in ocean fish, beef, chicken, pork, sandwich meat, eggs, cheese, and ice cream, as well as human milk, were in the range O.33 to 0.51 ppt, wet weight. In whole dairy milk TEQ was 0.16 ppt, and in butter 1.1 ppt. Mean daily intake of TEQ for U.S. breast-fed infants during the first year of life was estimated at 42 pg/kg body weight. For children aged 1-11 yr the estimated daily TEQ intake was 6.2 pg/kg body weight. For males and females aged 12-19 yr, the estimated TEQ intake was 3.5 and 2.7 pg/kg body weight, respectively. For adult men and women aged 20-79 yr, estimated mean daily TEQ intakes were 2.4 and 2.2 pg/kg body weight, respectively. Estimated mean daily intake of TEQ declined with age to a low of 1.9 pg/kg body weight at age 80 yr and older. For all ages except 80 yr and over, estimates were higher for males than females. For adults, dioxins, dibenzofurans, and PCBs contributed 42%, 30%, and 28% of dietary TEQ intake, respectively. DDE was also analyzed in the pooled food samples.

Adolescent↗
PubMed2001

Pathogenicity of a natural recombinant associated with ageratum yellow vein disease: implications for geminivirus evolution and disease aetiology.

Yellow vein disease of Ageratum conyzoides is caused by a viral DNA complex consisting of the genomic component (DNA A) of the monopartite begomovirus Ageratum yellow vein virus (AYVV, family: Geminiviridae) and a small satellite-like DNA beta component. AYVV DNA A is unable to induce symptoms in this host alone but can systemically infect A. conyzoides in which it accumulates to low levels. Here, we demonstrate that the yellow vein phenotype can also be produced by co-inoculating A. conyzoides with AYVV DNA A and recDNA-Abeta17, a naturally occurring recombinant of approximately the same size as DNA beta that contains sequences from both DNA A and DNA beta. Symptoms induced by DNA A and recDNA-Abeta17 in A. conyzoides and Nicotiana glutinosa are qualitatively similar to those associated with DNA A and DNA beta although milder. Recombination between DNA A and DNA beta to produce a chimera resembling recDNA-Abeta17 was observed after whitefly transmission of the disease in A. conyzoides. Hence, such recombination events are likely to occur frequently, implying that recombinants will normally be associated with this type of disease complex in the field. Possible implications of these findings for the evolution of begomoviruses and the aetiology of their diseases are discussed.

Asteraceae↗
PubMed2001

Fluorescent amplified fragment length polymorphism genotyping of Salmonella Enteritidis: a method suitable for rapid outbreak recognition.

OBJECTIVE: To perform fluorescent amplified fragment length polymorphism (FAFLP) analysis on phage type (PT) reference strains of Salmonella enterica subsp. enterica serotype Enteritidis (S. Enteritidis), and S. Enteritidis PT 6 and 6a recent clinical isolates to determine its usefulness for primary characterization of clinical S. Enteritidis isolates, and then to determine whether FAFLP is suitable for rapid characterization of strains in an outbreak situation. METHODS: Twenty-five PT reference strains of S. Enteritidis and 20 S. Enteritidis PT 6 and 6a clinical isolates were subjected to FAFLP analysis using the selective primer combinations Eco + 0-Mse + T and Eco + 0-Mse + TA. RESULTS: FAFLP successfully separated each one of the 25 S. Enteritidis PT strains into distinct profiles, while macrorestriction and PFGE using XbaI identified 20 pulsed-field profiles. FAFLP also resolved cases and outbreaks due to S. Enteritidis PTs 6 and 6a. CONCLUSIONS: The resolving power of FAFLP was higher than that of PFGE. FAFLP is a highly discriminatory genotyping method and, in conjunction with phage typing for primary subdivision of S. Enteritidis, provides a rapid and powerful tool for strain differentiation, both for outbreak investigation and for epidemiologic surveillance.

Bacterial Typing Techniques↗
PubMed2001

Gene C2 of the monopartite geminivirus tomato yellow leaf curl virus-China encodes a pathogenicity determinant that is localized in the nucleus.

Expression of the Tomato yellow leaf curl virus-China (TYLCV-C) C2 protein and green fluorescent protein (GFP) fused to the C2 protein (C2-GFP) in Nicotiana benthamiana from a Potato virus X (PVX) vector induced necrotic ringspots on inoculated leaves as well as necrotic vein banding and severe necrosis on systemically infected leaves. The localization of GFP fluorescence in plant cells infected with PVX/C2-GFP and in insect cells transfected with Baculovirus expressing C2-GFP indicates that the TYLCV-C C2 protein is capable of shuttling GFP into plant and insect cell nuclei. Our data demonstrate that the TYLCV-C C2 protein may contribute to viral pathogenicity in planta and is nuclear localized.

Amino Acid Sequence↗
PubMed2001

Campylobacter hominis sp. nov., from the human gastrointestinal tract.

Sequences of 16S rDNA of a novel campylobacter from faeces of healthy humans were previously shown to originate from a new taxon, 'Candidatus Campylobacter hominis', which could not be cultured. Since phylogenetic analysis suggested that anaerobic conditions might be required for growth, an isolation strategy was developed employing initial non-selective membrane filtration onto fastidious anaerobe agar. Campylobacters were then isolated from the resulting mixed microbial flora by a dilution strategy and/or by immunomagnetic separation with genus-specific polyclonal antibody. Isolates were identified by a genus and taxon-specific PCR assay, and 16S rDNA nucleotide sequence analysis was carried out. All isolates exhibited the typical Campylobacter characteristics of being non-fermentative, oxidase-positive, catalase-negative and Gram-negative. Unusually, however, they were straight rods lacking flagella. The 16S rDNA nucleotide sequence analysis, DNA and mol% G+C were consistent with a new Campylobacter species whose nearest phylogenetic neighbours were Campylobacter gracilis and Campylobacter sputorum. The unique species status of the isolates was further confirmed by taxonomic analysis of 47 phenotypic characteristics. The name Campylobacter hominis sp. nov. is proposed for the new species, the type strain of which is NCTC 13146T (= LMG 19568T).

Bacterial Typing Techniques↗
PubMed2001

Fluorescent amplified-fragment length polymorphism subtyping of the Salmonella enterica serovar enteritidis phage type 4 clone complex.

Fluorescent amplified-fragment length polymorphism (FAFLP) analysis, a high-resolution PCR-based genome fingerprinting method, was used to subtype Salmonella enterica serovar Enteritidis phage type 4. This single phage type is responsible for the majority of salmonellosis in Europe. Twenty strains isolated from nine outbreaks, five isolates from sporadic cases of human infection, four strains of poultry origin, and one laboratory-derived strain were comparatively studied by pulsed-field gel electrophoresis (PFGE) and FAFLP analysis. Following macrorestriction with XbaI, PFGE classified 73% of PT4 strains as a single type. FAFLP analysis was carried out with the primer pair EcoRI+0 and MseI+C, by simultaneously sampling 170 to 190 loci throughout the PT4 genome. Twenty-three FAFLP profiles, with 1 to 61 amplified-fragment differences, were found among the 30 strains. The index of discriminatory power of FAFLP analysis was 0.98, compared to 0.47 for PFGE. FAFLP analysis assigned genotypes to each PT4 outbreak, as well as sporadic PT4 infections, a significant development for the epidemiology and control of this zoonotic enteric pathogen.

Animals↗
PubMed2001

Genome sequence-based fluorescent amplified fragment length polymorphism of Campylobacter jejuni, its relationship to serotyping, and its implications for epidemiological analysis.

The published genome sequence of Campylobacter jejuni strain NCTC 11168 was used to model an accurate and highly reproducible fluorescent amplified fragment length polymorphism (FAFLP) analysis. Predicted and experimentally observed amplified fragments (AFs) generated with the primer pair HindIII+A and HhaI+A were compared. All but one of the 61 predicted AFs were reproducibly detected, and no unpredicted fragments were amplified. This FAFLP analysis was used to genotype 74 C. jejuni strains belonging to the nine heat-stable (HS) serotypes most prevalent in human disease in England and Wales. The 74 C. jejuni strains exhibited 60 FAFLP profiles, and cluster analysis of them yielded a radial tree showing genetic relationships between and within 13 major clusters. Some clusters were related, and others were unrelated, to a single HS serotype. For example, all strains belonging to serotypes HS6 and HS19 grouped into corresponding single genotypic clusters, while strains of serotypes HS11 and HS18 each grouped into two genotypic clusters. Strains of HS50, the most prevalent serotype infecting humans, were found both in one large (multiserotype) cluster complex and dispersed throughout the tree. The strain genotypes within each FAFLP cluster were characterized by a particular combination of AFs, and among the cluster there were additional differential AFs. Identification of such AFs could act as a search tool to look for potential associations with disease or animal hosts, when applied to large number of human isolates. Genome-sequence based FAFLP, thus, has the potential to establish a genetic database for epidemiological investigations of Campylobacter.

Animals↗