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61.
Richard T. Blankley Christal Fisher Melissa Westwood Robyn North Philip N. Baker Michael J. Walker Andrew Williamson Anthony D. Whetton Wanchang Lin Lesley McCowan Claire T. Roberts Garth J. S. Cooper Richard D. Unwin Jenny E. Myers 《Molecular & cellular proteomics : MCP》2013,12(11):3148-3159
Pre-eclampsia (PE) is a serious complication of pregnancy with potentially life threatening consequences for both mother and baby. Presently there is no test with the required performance to predict which healthy first-time mothers will go on to develop PE. The high specificity, sensitivity, and multiplexed nature of selected reaction monitoring holds great potential as a tool for the verification and validation of putative candidate biomarkersfor disease states. Realization of this potential involves establishing a high throughput, cost effective, reproducible sample preparation workflow. We have developed a semi-automated HPLC-based sample preparation workflow before a label-free selected reaction monitoring approach. This workflow has been applied to the search for novel predictive biomarkers for PE.To discover novel candidate biomarkers for PE, we used isobaric tagging to identify several potential biomarker proteins in plasma obtained at 15 weeks gestation from nulliparous women who later developed PE compared with pregnant women who remained healthy. Such a study generates a number of “candidate” biomarkers that require further testing in larger patient cohorts. As proof-of-principle, two of these proteins were taken forward for verification in a 100 women (58 PE, 42 controls) using label-free SRM. We obtained reproducible protein quantitation across the 100 samples and demonstrated significant changes in protein levels, even with as little as 20% change in protein concentration. The SRM data correlated with a commercial ELISA, suggesting that this is a robust workflow suitable for rapid, affordable, label-free verification of which candidate biomarkers should be taken forward for thorough investigation. A subset of pregnancy-specific glycoproteins (PSGs) had value as novel predictive markers for PE.The identification of clinically relevant plasma biomarkers with diagnostic and/or predictive value continues to challenge the proteomics field. Whereas once the biomarker pipeline was described as a two part discovery and validation process, there is increasing consensus that an intermediate step is required in which the proteins identified in the discovery phase are technically verified in 50 to 200 samples. This verification step identifies false positives from the discovery phase and allows prioritization of proteins to be taken into large-scale clinical validation studies (1). Although commercial ELISA kits may be used in this phase, these are unavailable for many proteins, are expensive, and may lack specificity. In addition, sample requirements may be too high to perform ELISA on all candidates, especially if many proteins are identified as potential markers by low powered, high penetration discovery workflows.Selected reaction monitoring (SRM)1 mass spectrometry has great potential as an alternative verification method (2–6) as it can be multiplexed, customized, and is highly specific. This potential has not been exploited to date, largely because of technical issues developing a low-cost, reproducible workflow encompassing plasma and serum preparation and LC/MS analysis with the capability to measure protein levels reproducible in hundreds of samples. With traditional stable isotope dilution SRM (SID-SRM), the high cost of accurately quantified, purified stable isotope encoded peptides or proteins may be prohibitive for the verification of multiple peptides from many proteins. Label-free relatively quantitative methods are increasingly popular in discovery proteomics but to a much lesser extent in targeted SRM studies (7, 8).For any SRM method, sample preparation workflows must balance the extent of enrichment and fractionation to enable quantification of lower abundance proteins, against increased technical variability (which is influenced by the number of sample handling steps) and reduced multiplexed potential as a consequence of fractionating peptides from the protein of interest into several distinct fractions. It is also essential that the true technical variation in the workflow is quantitatively evaluated from freezer to MS analysis, rather than just the variation within the LC-SRM part of the experiment. As a paradigm for a label-free SRM assay, we developed our workflow and applied it to the verification of candidate biomarkers that indicate the risk of pre-eclampsia (PE).PE affects 2–8% of pregnancies, and is characterized by hypertension and proteinuria, which may progress to severe maternal complications or death (9). Because delivery of the infant is the only effective intervention, a third of babies are born premature and fetal or newborn mortality is increased three- to 10-fold (10). Its complex etiology involves abnormal placentation, an altered immune response and a sensitized maternal vascular endothelium (11). Prediction of the condition in early pregnancy would allow prevention strategies, such as low dose aspirin, to be targeted to high risk women. In first-time pregnant women, a group particularly at risk, biomarkers continue to fall short of a test that would be useful or cost effective in clinical practice (12–14). Better-performing novel biomarkers are required.The aim of this study was to identify candidate predictive biomarkers for PE and then develop a verification assay using mass spectrometry to determine whether these should be taken forward into more extensive and expensive validation studies. Initial discovery experiments were employed using a pooled sample iTRAQ approach using two different MS platforms to increase plasma proteome coverage. Among the set of proteins discovered, we then developed a label-free SRM assay for relative quantification of CXCL7 (Platelet basic protein; PBP) and members of the Pregnancy specific glycoprotein (PSG) family in a 100-sample set from the international SCreeningfOr Pregnancy Endpoints (SCOPE) study (www.scopestudy.net). Our workflow allowed the specificity and linearity of response for each peptide to be determined, along with true technical variability. Although absolute concentration and LOD/LOQ cannot be calculated using this approach, we aimed to test the hypothesis that a label-free SRM approach could provide a rapid, robust, and efficient screen of candidate plasma biomarkers. 相似文献
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65.
Alphonse Ouédraogo Alfred B. Tiono Désiré Kargougou Jean Baptiste Yaro Esperance Ouédraogo Youssouf Kaboré David Kangoye Edith C. Bougouma Adama Gansane Noelie Henri Amidou Diarra Souleymane Sanon Issiaka Soulama Amadou T. Konate Nora L. Watson Valerie Brown Jenny Hendriks Maria Grazia Pau Isabella Versteege Edison Wiesken Jerald Sadoff Issa Nebie Sodiomon B. Sirima 《PloS one》2013,8(11)
Background
Ad35.CS.01 is a pre-erythrocytic malaria candidate vaccine. It is a codon optimized nucleotide sequence representing the P. falciparum circumsporozoite (CS) surface antigen inserted in a replication deficient Adenovirus 35 backbone. A Phase 1a trial has been conducted in the USA in naïve adults and showed that the vaccine was safe. The aim of this study is to assess the safety and immunogenicity of ascending dosages in sub Saharan Africa.Methods
A double blind, randomized, controlled, dose escalation, phase Ib trial was conducted in a rural area of Balonghin, the Saponé health district (Burkina Faso). Forty-eight healthy adults aged 18-45 years were randomized into 4 cohorts of 12 to receive three vaccine doses (day 0, 28 and 84) of 109, 1010, 5X1010, 1011 vp of Ad35.CS.01 or normal saline by intra muscular injection. Subjects were monitored carefully during the 14 days following each vaccination for non serious adverse events. Severe and serious adverse events were collected throughout the participant study duration (12 months from the first vaccination). Humoral and cellular immune responses were measured on study days 0, 28, 56, 84, 112 and 140.Results
Of the forty-eight subjects enrolled, forty-four (91.7%) received all three scheduled vaccine doses. Local reactions, all of mild severity, occurred in thirteen (27.1%) subjects. Severe (grade 3) laboratory abnormalities occurred in five (10.4%) subjects. One serious adverse event was reported and attributed to infection judged unrelated to vaccine. The vaccine induced both antibody titers and CD8 T cells producing IFNγ and TNFα with specificity to CS while eliciting modest neutralizing antibody responses against Ad35.Conclusion
Study vaccine Ad35.CS.01 at four different dose levels was well-tolerated and modestly immunogenic in this population. These results suggest that Ad35.CS.01 should be further investigated for preliminary efficacy in human challenge models and as part of heterologous prime-boost vaccination strategies.Trial Registration
ClinicalTrials.gov NCT01018459 http://clinicaltrials.gov/ct2/show/NCT01018459 相似文献66.
Helge Niemann Peter Linke Katrin Knittel Enrique MacPherson Antje Boetius Warner Brückmann Gaute Larvik Klaus Wallmann Ulrike Schacht Enoma Omoregie David Hilton Kevin Brown Gregor Rehder 《PloS one》2013,8(10)
Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as −53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab''s nutrition. In addition, our lipid analyses also suggest that the crabs feed on other 13C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus. 相似文献
67.
It has been suggested that the process of domestication, at least in some species, has led to an innate predisposition to be skilled at reading human communicative and attentional cues. Adult domestic horses (Equus caballus) are highly sensitive to subtle bodily cues when determining if a person is attending to them but they are less adept at using human communicative cues in object choice tasks. Here we provide the first study into the ontogeny of such skills in order to gain insights into the mechanisms underlying these abilities. Compared with adult horses, youngsters under the age of three could use body orientation but not more subtle cues such as head movement and open/closed eyes to correctly choose an attentive person to approach for food. Across two object choice experiments, the performance of young horses was comparable to that of adult horses – subjects were able to correctly choose a rewarded bucket using marker placement, pointing and touching cues but could not use body orientation, gaze, elbow pointing or tapping cues. Taken together these results do not support the theory that horses possess an innate predisposition to be particularly skilled at using human cues. Horses'' ability to determine whether humans are attending to them using subtle body cues appears to require significant experience to fully develop and their perhaps less remarkable use of limited cues in object choice tasks, although present at a much earlier age, is likely to reflect a more general learning ability related to stimulus enhancement rather than a specific ‘human-reading’ skill. 相似文献
68.
Dimitrios Paraskevis Georgios Nikolopoulos Anastasios Fotiou Chrissa Tsiara Dimitra Paraskeva Vana Sypsa Marios Lazanas Panagiotis Gargalianos Mina Psichogiou Athanasios Skoutelis Lucas Wiessing Samuel R. Friedman Don C. d. e. s. Jarlais Manina Terzidou Jenny Kremastinou Meni Malliori Angelos Hatzakis 《PloS one》2013,8(11)
Background
During 2011, a dramatic increase (1600%) of reported HIV-1 infections among injecting drug users (IDUs) was noted in Athens, Greece. We herein assess the potential causal pathways associated with this outbreak.Methods
Our study employed high resolution HIV-1 phylogenetic and phylogeographic analyses. We examined also longitudinal data of ecological variables such as the annual growth of gross domestic product (GDP) of Greece in association with HIV-1 and HCV sentinel prevalence in IDUs, unemployment and homelessness rates and HIV transmission networks in Athens IDUs before and during economic recession (2008–2012).Results
IDU isolates sampled in 2011 and 2012 suggested transmission networks in 94.6% and 92.7% of the cases in striking contrast with the sporadic networking (5%) during 1998–2009. The geographic origin of most HIV-1 isolates was consistent with the recently documented migratory waves in Greece. The decline in GDP was inversely correlated with annual prevalence rates of HIV and HCV and with unemployment and homelessness rates in IDUs (all p<0.001). The slope of anti-HCV prevalence in the sentinel populations of IDUs and in “new” drug injectors was found 120 and 1.9-fold (p = 0.007, p = 0.08 respectively) higher in 2008–2012 (economic recession) compared with 2002–2006. The median (25th, 75th) size of transmission networks were 34 (12, 58) and 2 (2, 2) (p = 0.057) in 2008–2012 and 1998–2007, respectively. The coverage of harm reduction services was low throughout the study period.Conclusions
Scaling-up harm reduction services and addressing social and structural factors related to the current economic crisis should be urgently considered in environments where HIV-1 outbreaks may occur. 相似文献69.
Stephanie S. Gervasi Jenny Urbina Jessica Hua Tara Chestnut Rick A. Relyea Andrew R. Blaustein 《EcoHealth》2013,10(2):166-171
The emerging fungal pathogen, Batrachochytrium dendrobatidis (Bd), has been associated with global amphibian population declines and extinctions. American bullfrogs (Lithobates catesbeianus) are widely reported to be a tolerant host and a carrier of Bd that spreads the pathogen to less tolerant hosts. Here, we examined whether bullfrogs raised from eggs to metamorphosis in outdoor mesocosms were susceptible to Bd. We experimentally exposed metamorphic juveniles to Bd in the laboratory and compared mortality rates of pathogen-exposed animals to controls (non-exposed) in two separate experiments; one using a Bd strain isolated from a Western toad and another using a strain isolated from an American bullfrog. We wanted to examine whether metamorphic bullfrogs were susceptible to either of these strains. We show that bullfrogs were susceptible to one strain of Bd and not the other. In both experiments, infection load detected in the skin decreased over time, suggesting that metamorphic bullfrogs from some populations may be inefficient long-term carriers of Bd. 相似文献
70.
Steven A. Hawks Florent Deledalle Jizhong Yao Dylan G. Rebois Gang Li Jenny Nelson Yang Yang Thomas Kirchartz James R. Durrant 《Liver Transplantation》2013,3(9):1201-1209
We explore the interrelation between density of states, recombination kinetics, and device performance in efficient poly[4,8‐bis‐(2‐ethylhexyloxy)‐benzo[1,2‐b:4,5‐b']dithiophene‐2,6‐diyl‐alt‐4‐(2‐ethylhexyloxy‐1‐one)thieno[3,4‐b]thiophene‐2,6‐diyl]:[6,6]‐phenyl‐C71‐butyric acid methyl ester (PBDTTT‐C:PC71BM) bulk‐heterojunction organic solar cells. We modulate the active‐layer density of states by varying the polymer:fullerene composition over a small range around the ratio that leads to the maximum solar cell efficiency (50–67 wt% PC71BM). Using transient and steady‐state techniques, we find that nongeminate recombination limits the device efficiency and, moreover, that increasing the PC71BM content simultaneously increases the carrier lifetime and drift mobility in contrast to the behavior expected for Langevin recombination. Changes in electronic properties with fullerene content are accompanied by a significant change in the magnitude or energetic separation of the density of localized states. Our comprehensive approach to understanding device performance represents significant progress in understanding what limits these high‐efficiency polymer:fullerene systems. 相似文献