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Search Results: 1 - 10 of 206606 matches for " Andrew G. Parker "
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Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data
Nicolas J Parker, Andrew G Parker
Source Code for Biology and Medicine , 2008, DOI: 10.1186/1751-0473-3-5
Abstract: A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads.Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension.The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.The introduction of micro-fabricated high-density picolitre reactor pyrophosphate sequencing [1,2] by the company 454 Life Sciences (454 Life Sciences Corp., 20 Commercial Street, Branford, Connecticut 06405, USA; hereafter referred to as 454 sequencing) makes available for the first time large quantities of sequence data at reasonable cost. The continual reduction in sequencing cost will encourage sequencing by small groups or individual researchers with modest computer resources and limited experience of bioinformatics tools.The nature of the data from pyrophosphate sequencing is however both qualitatively and quantitatively different from that generated by Sanger sequencing [3] using fluorescent chain-terminating nucleotide analogues [4]. Instead of receiving a single consensus sequence with associated chromatogram (scf) file, this form of pyrophosphate sequencing generated for us 300 000 short sequence reads, around 100 bases long [5], assembled into several hundred contigs. However the normal system of ch
Radiation-induced sterility for pupal and adult stages of the malaria mosquito Anopheles arabiensis
Michelle EH Helinski, Andrew G Parker, Bart GJ Knols
Malaria Journal , 2006, DOI: 10.1186/1475-2875-5-41
Abstract: Pupae were irradiated shortly before emergence (at 22–26 hrs of age), and adults <24 hrs post emergence. Doses tested ranged between 0 and 100 Gy. The effects of irradiation on adult emergence, male survival, induced sterility and insemination capability were evaluated. Emergence and insemination data were analysed using independent t-tests against the control. Correlation analyses were performed for insemination rate and dose and insemination and fecundity. Male survival was analysed using Kaplan-Meier survival analyses. Finally, the calculated residual fertility values were inverse-normal transformed and linear regression analyses performed.Irradiation of pupae, for all doses tested, had no effect on adult emergence. Survival curves of males irradiated as pupae or adults were similar or even slightly higher than non-irradiated males. Overall, adults appeared to be slightly more susceptible to irradiation, although no significant differences for individual doses were observed. In the pupal stage, a significant negative correlation was found between insemination and dose, but the correlation-coefficient was associated with less than 25% of the total variation. A review of the literature indicated that An. arabiensis is more radiation resistant than other anopheline mosquitoes.The optimal dose for male insects to be released in an SIT programme depends on their level of sterility and competitiveness. The use of semi-sterilizing doses to produce more competitive insects is discussed. The most convenient developmental stage for mosquito irradiation on a mass-scale are pupae, but pupal irradiation resulted in a lower insemination rate at the highest dose compared to adult irradiation. On the basis of this study, a suitable dose range that includes semi-sterilizing doses is identified to initiate competitiveness experiments for males irradiated at both developmental stages.In the 21st century, anopheline mosquitoes remain the most deadly insects in the world. Malaria is
Radiation biology of mosquitoes
Helinski Michelle EH,Parker Andrew G,Knols Bart GJ
Malaria Journal , 2009, DOI: 10.1186/1475-2875-8-s2-s6
Abstract: There is currently renewed interest in assessing the feasibility of the sterile insect technique (SIT) to control African malaria vectors in designated areas. The SIT relies on the sterilization of males before mass release, with sterilization currently being achieved through the use of ionizing radiation. This paper reviews previous work on radiation sterilization of Anopheles mosquitoes. In general, the pupal stage was irradiated due to ease of handling compared to the adult stage. The dose-response curve between the induced sterility and log (dose) was shown to be sigmoid, and there was a marked species difference in radiation sensitivity. Mating competitiveness studies have generally been performed under laboratory conditions. The competitiveness of males irradiated at high doses was relatively poor, but with increasing ratios of sterile males, egg hatch could be lowered effectively. Males irradiated as pupae had a lower competitiveness compared to males irradiated as adults, but the use of partially-sterilizing doses has not been studied extensively. Methods to reduce somatic damage during the irradiation process as well as the use of other agents or techniques to induce sterility are discussed. It is concluded that the optimal radiation dose chosen for insects that are to be released during an SIT programme should ensure a balance between induced sterility of males and their field competitiveness, with competitiveness being determined under (semi-) field conditions. Self-contained 60Co research irradiators remain the most practical irradiators but these are likely to be replaced in the future by a new generation of high output X ray irradiators.
Tsetse Salivary Gland Hypertrophy Virus: Hope or Hindrance for Tsetse Control?
Adly M. M. Abd-Alla ,Andrew G. Parker,Marc J. B. Vreysen,Max Bergoin
PLOS Neglected Tropical Diseases , 2011, DOI: 10.1371/journal.pntd.0001220
Abstract: Many species of tsetse flies (Diptera: Glossinidae) are infected with a virus that causes salivary gland hypertrophy (SGH), and flies with SGH symptoms have a reduced fecundity and fertility. The prevalence of SGH in wild tsetse populations is usually very low (0.2%–5%), but higher prevalence rates (15.2%) have been observed occasionally. The successful eradication of a Glossina austeni population from Unguja Island (Zanzibar) using an area-wide integrated pest management approach with a sterile insect technique (SIT) component (1994–1997) encouraged several African countries, including Ethiopia, to incorporate the SIT in their national tsetse control programs. A large facility to produce tsetse flies for SIT application in Ethiopia was inaugurated in 2007. To support this project, a Glossina pallidipes colony originating from Ethiopia was successfully established in 1996, but later up to 85% of adult flies displayed symptoms of SGH. As a result, the colony declined and became extinct by 2002. The difficulties experienced with the rearing of G. pallidipes, epitomized by the collapse of the G. pallidipes colony originating from Ethiopia, prompted the urgent need to develop management strategies for the salivary gland hypertrophy virus (SGHV) for this species. As a first step to identify suitable management strategies, the virus isolated from G. pallidipes (GpSGHV) was recently sequenced and research was initiated on virus transmission and pathology. Different approaches to prevent virus replication and its horizontal transmission during blood feeding have been proposed. These include the use of antiviral drugs such as acyclovir and valacyclovir added to the blood for feeding or the use of antibodies against SGHV virion proteins. In addition, preliminary attempts to silence the expression of an essential viral protein using RNA interference will be discussed.
Is there a gap between recommended and ‘real world’ practice in the management of depression in young people? A medical file audit of practice
Sarah E Hetrick, Andrew Thompson, Kally Yuen, Sue Finch, Alexandra G Parker
BMC Health Services Research , 2012, DOI: 10.1186/1472-6963-12-178
Abstract: We aimed to investigate the gaps between guideline recommendations and clinical practice in the management of young people with depression by undertaking an audit of medical files in a catchment area public mental health service for 15 to 25 year olds in Melbourne, Australia.The results showed that the assessment and recording of depression severity to ensure appropriate treatment planning was not systematic nor consistent; that the majority of young people (74.5%) were prescribed an antidepressant before an adequate trial of psychotherapy was undertaken and that less than 50% were monitored for depression symptom improvement and antidepressant treatment emergent suicide related behaviours (35% and 30% respectively). Encouragingly 92% of first line prescriptions for those aged 18 years or under who were previously antidepressant-na?ve was for fluoxetine as recommended.This research has highlighted the need for targeted strategies to ensure effective implementation. These strategies might include practice system tools that allow for systematic monitoring of depression symptoms and adverse side effects, particularly suicide related behaviours. Additionally, youth specific psychotherapy that incorporates the most effective components for this age group, delivered in a youth friendly way would likely aid effective implementation of guideline recommendations for engagement in an adequate trial of psychotherapy before medication is initiated.
A micro-pool model for decision-related signals in visual cortical areas
Andrew J. Parker
Frontiers in Computational Neuroscience , 2013, DOI: 10.3389/fncom.2013.00115
Abstract: The study of sensory signaling in the visual cortex has been greatly advanced by the recording of neural activity simultaneously with the performance of a specific psychophysical task. Individual nerve cells may also increase their firing leading up to the particular choice or decision made on a single psychophysical trial. Understanding these signals is important because they have been taken as evidence that a particular nerve cell or group of nerve cells in the cortex is involved in the formation of the perceptual decision ultimately signaled by the organism. However, recent analyses show that the size of a decision-related change in firing in a particular neuron is not a secure basis for concluding anything about the contribution of a single neuron to the formation of a decision: rather the size of the decision-related firing is expected to be dominated by the extent to which the activation of a single neuron is correlated with the firing of the pool of neurons. The critical question becomes what defines membership of a population of neurons. This article presents the proposal that groups of neurons are naturally linked together by their connectivity, which in turn reflects the previous history of sensory stimulations. When a new psychophysical task is performed, a group of neurons relevant to the judgment becomes involved because the firing of some neurons in that group is strongly relevant to the task. This group of neurons is called a micro-pool. This article examines the consequences of such a proposal within the visual nervous system. The main focus is on the signals available from single neurons, but it argued that models of choice-related signals must scale up to larger numbers of neurons because MRI and MEG studies also show evidence of similar choice signals.
The Antiviral Drug Valacyclovir Successfully Suppresses Salivary Gland Hypertrophy Virus (SGHV) in Laboratory Colonies of Glossina pallidipes
Adly M.M. Abd-Alla, Henry Adun, Andrew G. Parker, Marc J.B. Vreysen, Max Bergoin
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038417
Abstract: Many species of tsetse flies are infected with a virus that causes salivary gland hypertrophy (SGH) symptoms associated with a reduced fecundity and fertility. A high prevalence of SGH has been correlated with the collapse of two laboratory colonies of Glossina pallidipes and colony maintenance problems in a mass rearing facility in Ethiopia. Mass-production of G. pallidipes is crucial for programs of tsetse control including the sterile insect technique (SIT), and therefore requires a management strategy for this virus. Based on the homology of DNA polymerase between salivary gland hypertrophy virus and herpes viruses at the amino acid level, two antiviral drugs, valacyclovir and acyclovir, classically used against herpes viruses were selected and tested for their toxicity on tsetse flies and their impact on virus replication. While long term per os administration of acyclovir resulted in a significant reduction of productivity of the colonies, no negative effect was observed in colonies fed with valacyclovir-treated blood. Furthermore, treatment of a tsetse colony with valacyclovir for 83 weeks resulted in a significant reduction of viral loads and consequently suppression of SGH symptoms. The combination of initial selection of SGHV-negative flies by non-destructive PCR, a clean feeding system, and valacyclovir treatment resulted in a colony that was free of SGH syndromes in 33 weeks. This is the first report of the use of a drug to control a viral infection in an insect and of the demonstration that valacyclovir can be used to suppress SGH in colonies of G. pallidipes.
The role of ALOX5AP, LTA4H and LTB4R polymorphisms in determining baseline lung function and COPD susceptibility in UK smokers
Asif S Tulah, Stuart G Parker, Miriam F Moffatt, Andrew J Wardlaw, Martin J Connolly, Ian Sayers
BMC Medical Genetics , 2011, DOI: 10.1186/1471-2350-12-173
Abstract: Eight ALOX5AP, six LTA4H and six LTB4R single nucleotide polymorphisms (SNPs) were genotyped in a UK Smoking Cohort (n = 992). Association with baseline lung function (FEV1 and FEV1/FVC ratio) was determined by linear regression. Logistic regression was used to compare smoking controls (n = 176) with spirometry-defined COPD cases (n = 599) and to more severe COPD cases (GOLD stage 3 and 4, n = 389).No association with ALOX5AP, LTA4H or LTB4R survived correction for multiple testing. However, we showed modest association with LTA4H rs1978331C (intron 11) with increased FEV1 (p = 0.029) and with increased FEV1/FVC ratio (p = 0.020).These data suggest that polymorphisms spanning ALOX5AP, LTA4H and the LTB4R locus are not major determinants of baseline lung function in smokers, but provide tentative evidence for LTA4H rs1978331C (intron 11) in determining baseline FEV1 and FEV1/FVC ratio in Caucasian Smokers in addition to our previously identified role in asthma susceptibility.Chronic obstructive pulmonary disease (COPD) is a complex respiratory disease with genetic and environmental contributors to pathophysiology [1,2]. Evidence suggests the dihydroxy leukotriene, leukotriene B4 (LTB4), plays a role in this disease as its production is elevated in the airways of COPD subjects [3,4]. The altered inflammatory response of the airways of COPD sufferers is a result of lymphocytes and neutrophils, suggested in part to be the result of cigarette smoke inhalation [5]. Importantly, LTB4 has been shown to have chemotactic activity recruiting inflammatory cells to the lung [6,7]. LTB4 is implicated in the neutrophillic inflammation of COPD and has been suggested as the major chemotactic agent in more severe forms of this disease [8]. It has been established that the cysteinyl leukotrienes (CysLTs; LTC4, LTD4 and LTE4) play a significant role in bronchoconstriction and airway inflammation in asthma [9] but their role in COPD is less clear.Studies have suggested that polymorphism
Impact of Salivary Gland Hypertrophy Virus Infection on the Mating Success of Male Glossina pallidipes: Consequences for the Sterile Insect Technique
Gratian N. Mutika, Carmen Marin, Andrew G. Parker, Drion G. Boucias, Marc J. B. Vreysen, Adly M. M. Abd-Alla
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042188
Abstract: Many species of tsetse flies are infected by a virus (GpSGHV) that causes salivary gland hypertrophy (SGH). Female Glossina pallidipes (Austen) with SGH symptoms (SGH+) have reduced fecundity and SGH+ male G. pallidipes are unable to inseminate female flies. Consequently, G. pallidipes laboratory colonies with a high prevalence of SGH have been difficult to maintain and have collapsed on several occasions. To assess the potential impact of the release of SGH+ sterile male G. pallidipes on the efficacy of an integrated control programme with a sterile insect technique (SIT) component, we examined the mating efficiency and behaviour of male G. pallidipes in field cages in relation to SGH prevalence. The results showed in a field cage setting a significantly reduced mating frequency of 19% for a male G. pallidipes population with a high prevalence of SGH (83%) compared to 38% for a male population with a low prevalence of SGH (7%). Premating period and mating duration did not vary significantly with SGH status. A high percentage (>80%) of females that had mated with SGH+ males had empty spermathecae. The remating frequency of female G. pallidipes was very low irrespective of the SGH status of the males in the first mating. These results indicate that a high prevalence of SGH+ in G. pallidipes not only affects colony stability and performance but, in view of their reduced mating propensity and competitiveness, releasing SGH+ sterile male G. pallidipes will reduce the efficiency of a sterile male release programme.
Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome
Drion G. Boucias, Henry M. Kariithi, Kostas Bourtzis, Daniela I. Schneider, Karen Kelley, Wolfgang J. Miller, Andrew G. Parker, Adly M. M. Abd-Alla
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061150
Abstract: The vertically transmitted endosymbionts (Sodalis glossinidius and Wigglesworthia glossinidia) of the tsetse fly (Diptera: Glossinidae) are known to supplement dietary deficiencies and modulate the reproductive fitness and the defense system of the fly. Some tsetse fly species are also infected with the bacterium, Wolbachia and with the Glossina hytrosavirus (GpSGHV). Laboratory-bred G. pallidipes exhibit chronic asymptomatic and acute symptomatic GpSGHV infection, with the former being the most common in these colonies. However, under as yet undefined conditions, the asymptomatic state can convert to the symptomatic state, leading to detectable salivary gland hypertrophy (SGH+) syndrome. In this study, we investigated the interplay between the bacterial symbiome and GpSGHV during development of G. pallidipes by knocking down the symbionts with antibiotic. Intrahaemocoelic injection of GpSGHV led to high virus titre (109 virus copies), but was not accompanied by either the onset of detectable SGH+, or release of detectable virus particles into the blood meals during feeding events. When the F1 generations of GpSGHV-challenged mothers were dissected within 24 h post-eclosion, SGH+ was observed to increase from 4.5% in the first larviposition cycle to >95% in the fourth cycle. Despite being sterile, these F1 SGH+ progeny mated readily. Removal of the tsetse symbiome, however, suppressed transgenerational transfer of the virus via milk secretions and blocked the ability of GpSGHV to infect salivary glands of the F1 progeny. Whereas GpSGHV infects and replicates in salivary glands of developing pupa, the virus is unable to induce SGH+ within fully differentiated adult salivary glands. The F1 SGH+ adults are responsible for the GpSGHV-induced colony collapse in tsetse factories. Our data suggest that GpSGHV has co-evolved with the tsetse symbiome and that the symbionts play key roles in the virus transmission from mother to progeny.
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