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1.  Function in the Human Connectome: Task-fMRI and Individual Differences in Behavior 
NeuroImage  2013;80:169-189.
The primary goal of the Human Connectome Project (HCP) is to delineate the typical patterns of structural and functional connectivity in the healthy adult human brain. However, we know that there are important individual differences in such patterns of connectivity, with evidence that this variability is associated with alterations in important cognitive and behavioral variables that affect real world function. The HCP data will be a critical stepping-off point for future studies that will examine how variation in human structural and functional connectivity play a role in adult and pediatric neurological and psychiatric disorders that account for a huge amount of public health resources. Thus, the HCP is collecting behavioral measures of a range of motor, sensory, cognitive and emotional processes that will delineate a core set of functions relevant to understanding the relationship between brain connectivity and human behavior. In addition, the HCP is using task-fMRI (tfMRI) to help delineate the relationships between individual differences in the neurobiological substrates of mental processing and both functional and structural connectivity, as well as to help characterize and validate the connectivity analyses to be conducted on the structural and functional connectivity data. This paper describes the logic and rationale behind the development of the behavioral, individual difference, and tfMRI batteries and provides preliminary data on the patterns of activation associated with each of the fMRI tasks, at both a group and individual level.
PMCID: PMC4011498  PMID: 23684877
Cognitive; Emotion; Sensory and Motor Function; Individual Differences; Task-fMRI; Personality; Connectivity
2.  Seasonal variation in telomere length of a hibernating rodent 
Biology Letters  2013;9(2):20121095.
Small hibernating rodents have greater maximum lifespans and hence appear to age more slowly than similar-sized non-hibernators. We tested for a direct effect of hibernation on somatic maintenance and ageing by measuring seasonal changes in relative telomere length (RTL) in the edible dormouse Glis glis. Average RTL in our population did not change significantly over the hibernation season, and a regression model explaining individual variation in post-hibernation RTL suggested a significant negative effect of the reduction in body mass over the inactive hibernation period (an index of time spent euthermic), supporting the idea that torpor slows ageing. Over the active season, RTL on average decreased in sub-adults but increased in adults, supporting previous findings of greater telomere shortening at younger ages. Telomere length increase might also have been associated with reproduction, which occurred only in adults. Our study reveals how seasonal changes in physiological state influence the progress of life-history traits, such as somatic maintenance and ageing, in a small hibernating rodent.
PMCID: PMC3639760  PMID: 23389666
hibernation; ageing; dormouse; torpor
3.  Social Isolation Shortens Telomeres in African Grey Parrots (Psittacus erithacus erithacus) 
PLoS ONE  2014;9(4):e93839.
Telomeres, the caps of eukaryotic chromosomes, control chromosome stability and cellular senescence, but aging and exposure to chronic stress are suspected to cause attrition of telomere length. We investigated the effect of social isolation on telomere length in the highly social and intelligent African Grey parrot (Psittacus erithacus erithacus). Our study population consisted of single-housed (n = 26) and pair-housed (n = 19) captive individuals between 0.75 to 45 years of age. Relative telomere length of erythrocyte DNA was measured by quantitative real-time PCR. We found that telomere length declined with age (p<0.001), and socially isolated parrots had significantly shorter telomeres compared to pair-housed birds (p<0.001) – even among birds of similar ages. Our findings provide the first evidence that social isolation affects telomere length, which supports the hypothesis that telomeres provide a biomarker indicating exposure to chronic stress.
PMCID: PMC3976323  PMID: 24705445
4.  Comparison of Cell Expression Formats for the Characterization of GABAA Channels Using a Microfluidic Patch Clamp System 
Ensemble recording and microfluidic perfusion are recently introduced techniques aimed at removing the laborious nature and low recording success rates of manual patch clamp. Here, we present assay characteristics for these features integrated into one automated electrophysiology platform as applied to the study of GABAA channels. A variety of cell types and methods of GABAA channel expression were successfully studied (defined as IGABA>500 pA), including stably transfected human embryonic kidney (HEK) cells expressing α1β3γ2 GABAA channels, frozen ready-to-assay (RTA) HEK cells expressing α1β3γ2 or α3β3γ2 GABAA channels, transiently transfected HEK293T cells expressing α1β3γ2 GABAA channels, and immortalized cultures of human airway smooth muscle cells endogenously expressing GABAA channels. Current measurements were successfully studied in multiple cell types with multiple modes of channel expression in response to several classic GABAA channel agonists, antagonists, and allosteric modulators. We obtained success rates above 95% for transiently or stably transfected HEK cells and frozen RTA HEK cells expressing GABAA channels. Tissue-derived immortalized cultures of airway smooth muscle cells exhibited a slightly lower recording success rate of 75% using automated patch, which was much higher than the 5% success rate using manual patch clamp technique by the same research group. Responses to agonists, antagonists, and allosteric modulators compared well to previously reported manual patch results. The data demonstrate that both the biophysics and pharmacologic characterization of GABAA channels in a wide variety of cell formats can be performed using this automated patch clamp system.
PMCID: PMC3419985  PMID: 22574655
5.  RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species 
BMC Genomics  2013;14:375.
Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS), genomes and transcriptomes of virtually any species are now available for studies of adaptive evolution. We experimentally manipulated temperature conditions for two groups of crimson spotted rainbowfish (Melanotaenia duboulayi) and measured differences in RNA transcription between them. This non-migratory species is found across a latitudinal thermal gradient in eastern Australia and is predicted to be negatively impacted by ongoing environmental and climatic change.
Using next generation RNA-seq technologies on an Illumina HiSeq2000 platform, we assembled a de novo transcriptome and tested for differential expression across the treatment groups. Quality of the assembly was high with a N50 length of 1856 bases. Of the 107,749 assembled contigs, we identified 4251 that were differentially expressed according to a consensus of four different mapping and significance testing approaches. Once duplicate isoforms were removed, we were able to annotate 614 up-regulated transfrags and 349 that showed reduced expression in the higher temperature group.
Annotated blast matches reveal that differentially expressed genes correspond to critical metabolic pathways previously shown to be important for temperature tolerance in other fish species. Our results indicate that rainbowfish exhibit predictable plastic regulatory responses to temperature stress and the genes we identified provide excellent candidates for further investigations of population adaptation to increasing temperatures.
PMCID: PMC3680095  PMID: 23738713
Rainbowfish; Melanotaenia duboulayi; Transcriptomes; Climate change; Thermal adaptation
6.  Daily torpor is associated with telomere length change over winter in Djungarian hamsters 
Biology Letters  2011;8(2):304-307.
Ageing can progress at different rates according to an individual's physiological state. Natural hypothermia, including torpor and hibernation, is a common adaptation of small mammals to survive intermittent or seasonal declines in environmental conditions. In addition to allowing energy savings, hypothermia and torpor have been associated with retarded ageing and increased longevity. We tested the hypothesis that torpor use slows ageing by measuring changes in the relative telomere length (RTL) of Djungarian hamsters, Phodopus sungorus, a highly seasonal rodent using spontaneous daily torpor, over 180 days of exposure to a short-day photoperiod and warm (approx. 20°C) or cold (approx. 9°C) air temperatures. Multi-model inference showed that change in RTL within individuals was best explained by positive effects of frequency of torpor use, particularly at low body temperatures, as well as the change in body mass and initial RTL. Telomere dynamics have been linked to future survival and proposed as an index of rates of biological ageing. Our results therefore support the hypothesis that daily torpor is associated with physiological changes that increase somatic maintenance and slow the processes of ageing.
PMCID: PMC3297381  PMID: 21920955
ageing; hypothermia; senescence; torpor; telomere
7.  Development and Validation of a Brief Self-Report Measure of Trauma Exposure: The Trauma History Screen 
Psychological assessment  2011;23(2):463-477.
Although information about individuals’ exposure to highly stressful events such as traumatic stressors is often very useful for clinicians and researchers, available measures are too long and complex for use in many settings. The Trauma History Screen was developed to provide a very brief and easy-to-complete self-report measure of exposure to high magnitude stressor (HMS) events and of events associated with significant and persisting posttraumatic distress (PPD). The measure assesses the frequency of HMS and PPD events, and it provides detailed information about PPD events. Test-retest reliability was studied in four samples, and temporal stability was good to excellent for items and trauma types and excellent for overall HMS and PPD scores. Comprehensibility of items was supported by expert ratings of how well items appeared to be understood by participants with relatively low reading levels. In five samples, construct validity was supported by findings of strong convergent validity with a longer measure of trauma exposure and by correlations of HMS and PPD scores with PTSD symptoms. The psychometric properties of the THS appear to be comparable or better than longer and more complex measures of trauma exposure.
PMCID: PMC3115408  PMID: 21517189
traumatic stress; trauma; traumatic stressors; PTSD; posttraumatic; measurement; screen
8.  Evaluating the effectiveness of GP endorsement on increasing participation in the NHS Bowel Cancer Screening Programme in England: study protocol for a randomized controlled trial 
Trials  2012;13:18.
The success and cost-effectiveness of bowel cancer screening depends on achieving and maintaining high screening uptake rates. The involvement of GPs in screening has been found to improve patient compliance. Therefore, the endorsement of screening by GPs may increase uptake rates amongst non-responders.
A two-armed randomised controlled trial will evaluate the effectiveness of a GP endorsed reminder in improving patient participation in the NHS Bowel Cancer Screening Programme (NHSBCSP). Up to 30 general practices in the West Midlands with a screening uptake rate of less than 50% will be recruited and patients identified from the patient lists of these practices. Eligible patients will be those aged 60 to 74, who have previously been invited to participate in bowel screening but who have been recorded by the Midlands and North West Bowel Cancer Screening Hub as non-responders. Approximately 4,380 people will be randomised in equal numbers to either the intervention (GP letter and duplicate FOBt kit) or control (no additional contact) arms of the trial.
The primary outcome measure will be the difference in the uptake rate of FOBt screening for bowel cancer between the intervention and control groups at 13 weeks after the GP endorsed reminder and duplicate FOBt kit are sent. Secondary outcome measures will be subgroup analyses of uptake according to gender, age and deprivation quartile, and the validation of methods for collecting GP, NHSBCSP and patient costs associated with the intervention. Qualitative work (30 to 40 semi-structured interviews) will be undertaken with individuals in the intervention arm who return a FOBt kit, to investigate the relative importance of the duplicate FOBt kit, reminder to participate, and GP endorsement of that reminder in contributing to individuals' decisions to participate in screening.
Implementing feasible, acceptable and cost-effective strategies to improve screening uptake amongst non-responders to invitations to participate is fundamentally important for the success of screening programmes. If this feasibility study demonstrates a significant increase in uptake of FOBt screening in individuals receiving the intervention, a definitive, appropriately powered future trial will be designed.
Trial registration number
PMCID: PMC3305373  PMID: 22348399
Colorectal cancer; General practitioner; Screening; FOBt; Uptake; Non-responder; Randomised controlled trial; Qualitative; Endorsement
9.  Sex-specific selection for MHC variability in Alpine chamois 
In mammals, males typically have shorter lives than females. This difference is thought to be due to behavioural traits which enhance competitive abilities, and hence male reproductive success, but impair survival. Furthermore, in many species males usually show higher parasite burden than females. Consequently, the intensity of selection for genetic factors which reduce susceptibility to pathogens may differ between sexes. High variability at the major histocompatibility complex (MHC) genes is believed to be advantageous for detecting and combating the range of infectious agents present in the environment. Increased heterozygosity at these immune genes is expected to be important for individual longevity. However, whether males in natural populations benefit more from MHC heterozygosity than females has rarely been investigated. We investigated this question in a long-term study of free-living Alpine chamois (Rupicapra rupicapra), a polygynous mountain ungulate.
Here we show that male chamois survive significantly (P = 0.022) longer if heterozygous at the MHC class II DRB locus, whereas females do not. Improved survival of males was not a result of heterozygote advantage per se, as background heterozygosity (estimated across twelve microsatellite loci) did not change significantly with age. Furthermore, reproductively active males depleted their body fat reserves earlier than females leading to significantly impaired survival rates in this sex (P < 0.008). This sex-difference was even more pronounced in areas affected by scabies, a severe parasitosis, as reproductively active males were less likely to survive than females. However, we did not find evidence for a survival advantage associated with specific MHC alleles in areas affected by scabies.
Increased MHC class II DRB heterozygosity with age in males, suggests that MHC heterozygous males survive longer than homozygotes. Reproductively active males appear to be less likely to survive than females most likely because of the energetic challenge of the winter rut, accompanied by earlier depletion of their body fat stores, and a generally higher parasite burden. This scenario renders the MHC-mediated immune response more important for males than for females, which implies a relatively stronger selection pressure on MHC genes in males than in females.
PMCID: PMC3340304  PMID: 22335968
MHC; Sex-specific selection; Heterozygosity advantage; Alpine chamois
10.  Evolutionary genetics of MHC class II beta genes in the brown hare, Lepus europaeus 
Immunogenetics  2011;63(11):743-751.
The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. High levels of diversity at the MHC are thought to be the result of parasite-mediated selection and there is growing evidence to support this theory. Most studies, however, target just a single gene within the MHC and infer any evidence of selection to be representative of the entire gene region. Here we present data from three MHC class II beta genes (DPB, DQB, and DRB) for brown hares in two geographic regions and compare them against previous results from a class II alpha-chain gene (DQA). We report moderate levels of diversity and high levels of population differentiation in the DQB and DRB genes (Na = 11, Dest = 0.071 and Na = 15, Dest = 0.409, respectively), but not for the DPB gene (Na = 4, Dest = 0.00). We also detected evidence of positive selection within the peptide binding region of the DQB and DRB genes (95% CI, ω > 1.0) but found no signature of selection for DPB. Mutation and recombination were both found to be important processes shaping the evolution of the class II genes. Our findings suggest that while diversifying selection is a significant contributor to the generally high levels of MHC diversity, it does not act in a uniform manner across the entire MHC class II region. The beta-chain genes that we have characterized provide a valuable set of MHC class II markers for future studies of the evolution of adaptive variation in Leporids.
PMCID: PMC3190090  PMID: 21688061
DPB; DQB; DRB; MHC; Lepus europaeus; Selection
11.  Communication and proximity effects on outcomes attributable to sense of presence in distance bioinformatics education 
BMC Medical Education  2011;11:10.
Online learning is increasingly popular in medical education and sense of presence has been posited as a factor contributing to its success. Communication media influences on sense of presence and learning outcomes were explored in this study. Test performance and ratings of instruction and technology, factors influenced by sense of presence, are compared under four conditions involving different media and degrees of student physical presence: 1) videoconference co-located, 2) webcast co-located, 3) videoconference dispersed, and 4) webcast dispersed.
Eighty one first to forth year medical students heard a lecture on telemedicine and were asked to collaboratively search a telemedicine website under conditions where the lecture was delivered by videoconference or one way streaming (webcast) and where students were either co-located or dispersed. In the videoconference conditions, co-located students could use the technology to interact with the instructor and could interact with each other face to face, while the dispersed students could use the technology to interact with both the instructor and each other. In the webcast conditions, all students could use chat to communicate with the instructor or each other, although the co-located students also could interact orally. After hearing the lecture, students collaboratively searched a telemedicine website, took a test on lecture-website content and rated the instruction and the technology they used. Test scores on lecture and website content and ratings of instruction and technology for the four conditions were compared with analysis of variance and chi-square tests.
There were no significant differences in overall measures, although there were on selected ratings of instruction. Students in both webcast conditions indicated they were encouraged more to follow up on their own and felt instruction was more interactive than co-located videoconferencing students. Dispersed videoconferencing students indicated the highest levels of interaction and there was evidence they interacted more.
Results do not strongly support proximity as a sense of presence factor affecting performance and attitudes, but do suggest communication medium may affect interactivity.
PMCID: PMC3068129  PMID: 21401942
12.  Age-related changes in grey and white matter structure throughout adulthood 
Neuroimage  2010;51(3-2):943-951.
Normal ageing is associated with gradual brain atrophy. Determining spatial and temporal patterns of change can help shed light on underlying mechanisms. Neuroimaging provides various measures of brain structure that can be used to assess such age-related change but studies to date have typically considered single imaging measures. Although there is consensus on the notion that brain structure deteriorates with age, evidence on the precise time course and spatial distribution of changes is mixed. We assessed grey matter (GM) and white matter (WM) structure in a group of 66 adults aged between 23 and 81. Multimodal imaging measures included voxel-based morphometry (VBM)-style analysis of GM and WM volume and diffusion tensor imaging (DTI) metrics of WM microstructure. We found widespread reductions in GM volume from middle age onwards but earlier reductions in GM were detected in frontal cortex. Widespread age-related deterioration in WM microstructure was detected from young adulthood onwards. WM decline was detected earlier and more sensitively using DTI-based measures of microstructure than using markers of WM volume derived from conventional T1-weighted imaging.
PMCID: PMC2896477  PMID: 20211265
13.  An exploratory study of co-location as a factor in synchronous, collaborative medical informatics distance education 
BMC Research Notes  2010;3:30.
This study determined differences in learning, judgments of teaching and technology, and interaction when videoconferencing was used to deliver instruction on telemedicine to medical students in conditions where they were co-located and dispersed. A lecture on telemedicine was given by videoconference to medical students at a distant site. After a question and answer period, students were then given search problems on the topic and encouraged to collaborate. Half the students were randomly assigned to a co-located condition where they received the presentation and collaborated in a computer lab, and half were assigned to a dispersed condition where they were located in different rooms to receive the presentation and collaborate online using the videoconferencing technology. Students were observed in both conditions and they individually completed a test on presentation content and a rating scale about the quality of the teaching and the technology.
There were no differences between the two groups in the learning outcomes or judgments about the teaching and technology, with the exception that more students in the dispersed condition felt more interaction was fostered. The level and patterns of interaction were very different in the two conditions and higher for dispersed students.
Synchronous communication at a distance via videoconference may give sufficient sense of presence that the learning experience may be similar to that in actual classrooms, even when students are far apart. The technology may channel interaction in desirable ways.
PMCID: PMC2830947  PMID: 20181072
15.  EPR Line Shifts and Line Shape Changes Due to Spin Exchange of Nitroxide Free Radicals in Liquids 6. Separating Line Broadening due to Spin Exchange and Dipolar Interactions 
The journal of physical chemistry. A  2009;113(17):4930-4940.
EPR spectra of perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (PDT) are studied as functions of molar concentration, c, and temperature, T, in water and 70 wt% glycerol in water. The increase of the intrinsic linewidth averaged over the three hyperfine lines, 〈Btot〉, varies linearly with c with zero intercept in both solvents at all temperatures; therefore ddc〈Btot〉 is independent of c. The spin exchange induced dispersion, from which the spin exchange frequency, ωe, may be computed, increases linearly with 〈Btot〉, passing through the origin in water and in 70 % glycerol at high temperatures; however, at low temperatures, where dipolar interactions broaden the spectra, linearity does not prevail until 〈Btot〉 > 1 G due to a contribution of dipolar interactions to the dispersion. The broadening constant due to spin exchange, ddc〈Be〉, is found from the slope of the linear region, permitting a computation of the dipolar constant, ddcBdip=ddc〈Btot〉−ddc〈Be〉. Thus, the separation of concentration broadening into spin exchange and dipolar contributions is effected without having to appeal to some supposed temperature dependence of the two interactions. The fractional broadening by spin exchange, Ω(T), is near unity at high temperatures in both solvents, decreasing to zero in 70 % glycerol at 273 K. Ω(T) is a continuous function of the inverse rotational correlation time of PDT, but is discontinuous as a function of T/η where η is the shear viscosity. Ω(T) = 0.5, where spin exchange and dipolar interactions contribute equally to the linewidth occurs at T/η = 20 ± 1 K/cP in 70 % glycerol. Hydrodynamic predictions of ddc〈Be〉 via the Stokes-Einstein (SE) equation are remarkably accurate in 70 % glycerol comparable with the results in a series of alkanes. In water, ddc〈Be〉 is linear with T /η with zero intercept as required by the SE; however, with slope a factor of 0.73 smaller. ddc〈Bdip〉 is reasonably predicted by the SE only at very small values of η/T very quickly following an approximately logarithmic dependence rather that the linear prediction. Values of ddc〈Bdip〉 approach a plateau above η/T = 0.20 cP/K that is about one-half the solid state limit. Line shifts due to spin exchange are not yet useful to deduce values of Ω(T) due to a lack of knowledge of the time between re-encounters; however, they may be used to verify the values determined from line broadening and spin exchange induced dispersion. Some effects at low temperatures in 70% glycerol suggest that the effects of dipolar interaction are inadequately described by the widely accepted theory.
PMCID: PMC2790056  PMID: 19385676
16.  Sustained Weight Loss Following 12-Month Pramlintide Treatment as an Adjunct to Lifestyle Intervention in Obesity  
Diabetes Care  2008;31(9):1816-1823.
OBJECTIVE—To assess long-term weight loss efficacy and safety of pramlintide used at different dosing regimens and in conjunction with lifestyle intervention (LSI).
RESEARCH DESIGN AND METHODS—In a 4-month, double-blind, placebo-controlled, dose-ranging study, 411 obese subjects were randomized to receive pramlintide (six arms: 120, 240, and 360 μg b.i.d. and t.i.d.) or placebo in conjunction with a structured LSI program geared toward weight loss. Of the 4-month evaluable subjects (n = 270), 77% opted to continue preexisting treatment during an 8-month single-blind extension (LSI geared toward weight maintenance).
RESULTS—At month 4, mean weight loss from baseline in the pramlintide arms ranged from 3.8 ± 0.7 to 6.1 ± 0.8 kg (2.8 ± 0.8 kg with placebo). By month 12, initial 4-month weight loss was regained in the placebo group but was maintained in all but the 120-μg b.i.d. group. Placebo-corrected weight loss with 120 μg t.i.d. and 360 μg b.i.d. averaged 3.2 ± 1.2 kg (3.1 ± 1.1% body wt) and 3.3 ± 1.1 kg (3.1 ± 1.0% body wt), respectively, at month 4 (both P < 0.01; 4-month evaluable n = 270) and 6.1 ± 2.1 kg (5.6 ± 2.1% body wt) and 7.2 ± 2.3 kg (6.8 ± 2.3% body wt), respectively, at month 12 (both P < 0.01; 12-month evaluable n = 146). At month 12, 40 and 43% of subjects treated with 120 μg t.i.d. and 360 μg b.i.d., respectively, achieved ≥10% weight loss (vs. 12% for placebo). Nausea, the most common adverse event with pramlintide in the 4-month study (9–29% pramlintide vs. 2% placebo), was generally mild to moderate and occurred in <10% of subjects during the extension.
CONCLUSIONS—When used over 12 months as an adjunct to LSI, pramlintide treatment, with low-dose three-times-daily or higher-dose two-times-daily regimens, helped obese subjects achieve greater initial weight loss and enhanced long-term maintenance of weight loss.
PMCID: PMC2518351  PMID: 18753666
17.  Role of adiponectin in human skeletal muscle bioenergetics 
Cell metabolism  2006;4(1):75-87.
Insulin resistance is associated with impaired skeletal muscle oxidation capacity and reduced mitochondrial number and function. Here, we report that adiponectin signaling regulates mitochondrial bioenergetics in skeletal muscle. Individuals with a family history of type 2 diabetes display skeletal muscle insulin resistance and mitochondrial dysfunction; adiponectin levels strongly correlate with mtDNA content. Knockout of the adiponectin gene in mice is associated with insulin resistance and low mitochondrial content and reduced mitochondrial enzyme activity in skeletal muscle. Adiponectin treatment of human myotubes in primary culture induces mitochondrial biogenesis, palmitate oxidation, and citrate synthase activity, and reduces the production of reactive oxygen species. The inhibition of adiponectin receptor expression by siRNA, or of AMPK by a pharmacological agent, blunts adiponectin induction of mitochondrial function. Our findings define a skeletal muscle pathway by which adiponectin increases mitochondrial number and function and exerts antidiabetic effects.
PMCID: PMC2671025  PMID: 16814734
18.  Joie de vivre sans smokes 
PMCID: PMC1482760  PMID: 16818898
19.  The effects of sequence length and oligonucleotide mismatches on 5′ exonuclease assay efficiency 
Nucleic Acids Research  2002;30(20):e111.
Although increasingly used for DNA quantification, little is known of the dynamics of the 5′ exonuclease assay, particularly in relation to amplicon length and mismatches at oligonucleotide binding sites. In this study we used seven assays targeting the c-myc proto-oncogene to examine the effects of sequence length, and report a marked reduction in efficiency with increasing fragment length. Three of the assays were further tested on 15 mammalian species to gauge the effect of sequence differences on performance. We show that the effects of probe and primer binding site mismatches are complex, with single point mutations often having little effect on assay performance, while multiple mismatches to the probe caused the greatest reduction in efficiency. The usefulness of the assays in predicting rates of ‘allelic dropout’ and successful polymerase chain reactions (PCRs) in microsatellite genotyping studies is supported, and we demonstrate that the use of a fragment more similar in size to typical microsatellites (190 bp) is no more informative than a shorter (81 bp) fragment. The assays designed for this study can be used directly for quantification of DNA from many mammalian species or, alternatively, information provided here can be used to design unique sequence-specific assays to maximise assay efficiency.
PMCID: PMC137155  PMID: 12384613
21.  HLA-B*35-Restricted CD8+-T-Cell Epitope in Mycobacterium tuberculosis Rv2903c  
Infection and Immunity  2002;70(2):981-984.
Few human CD8+ T-cell epitopes in mycobacterial antigens have been described to date. Here we have identified a novel HLA-B*35-restricted CD8+ T-cell epitope in Mycobacterium tuberculosis Rv2903c based on a reverse immunogenetics approach. Peptide-specific CD8 T cells were able to kill M. tuberculosis-infected macrophages and produce gamma interferon and tumor necrosis factor alpha.
PMCID: PMC127663  PMID: 11796635
22.  Communal weeding 
Genome Biology  2000;1(6):reports4024.1-reports4024.3.
A report on the first annual Genomic Arabidopsis Resource Network (GARNet) meeting, York, UK, 2-3 October, 2000.
PMCID: PMC138889

Results 1-22 (22)