Journals
2012 EN
E. Ricky Chan · Didier Ménard · Peter H. David
+8 more
Background An estimated 2.85 billion people live at risk of Plasmodium vivax transmission. In endemic countries vivax malaria causes significant morbidity and its mortality is becoming more widely appreciated, drug-resistant strains are increasing in prevalence, and an increasing number of reports indicate that P. vivax is capable of breaking through the Duffy-negative barrier long considered to confer resistance to blood stage infection. Absence of robust in vitro propagation limits our understanding of fundamental aspects of the parasite's biology, including the determinants of its dormant hypnozoite phase, its virulence and drug susceptibility, and the molecular mechanisms underlying red blood cell invasion. Methodology/Principal Findings Here, we report results from whole genome sequencing of five P. vivax isolates obtained from Malagasy and Cambodian patients, and of the monkey-adapted Belem strain. We obtained an average 70–400 X coverage of each genome, resulting in more than 93% of the Sal I reference sequence covered by 20 reads or more. Our study identifies more than 80,000 SNPs distributed throughout the genome which will allow designing association studies and population surveys. Analysis of the genome-wide genetic diversity in P. vivax also reveals considerable allele sharing among isolates from different continents. This observation could be consistent with a high level of gene flow among parasite strains distributed throughout the world. Conclusions Our study shows that it is feasible to perform whole genome sequencing of P. vivax field isolates and rigorously characterize the genetic diversity of this parasite. The catalogue of polymorphisms generated here will enable large-scale genotyping studies and contribute to a better understanding of P. vivax traits such as drug resistance or erythrocyte invasion, partially circumventing the lack of laboratory culture that has hampered vivax research for years.
Public Library of Science
Journals
2012 EN
Peter W. Gething · Iqbal Elyazar · Catherine L. Moyes
+14 more
Background Current understanding of the spatial epidemiology and geographical distribution of Plasmodium vivax is far less developed than that for P. falciparum , representing a barrier to rational strategies for control and elimination. Here we present the first systematic effort to map the global endemicity of this hitherto neglected parasite. Methodology and Findings We first updated to the year 2010 our earlier estimate of the geographical limits of P. vivax transmission. Within areas of stable transmission, an assembly of 9,970 geopositioned P. vivax parasite rate ( Pv PR) surveys collected from 1985 to 2010 were used with a spatiotemporal Bayesian model-based geostatistical approach to estimate endemicity age-standardised to the 1–99 year age range ( Pv PR 1–99 ) within every 5×5 km resolution grid square. The model incorporated data on Duffy negative phenotype frequency to suppress endemicity predictions, particularly in Africa. Endemicity was predicted within a relatively narrow range throughout the endemic world, with the point estimate rarely exceeding 7% Pv PR 1–99 . The Americas contributed 22% of the global area at risk of P. vivax transmission, but high endemic areas were generally sparsely populated and the region contributed only 6% of the 2.5 billion people at risk (PAR) globally. In Africa, Duffy negativity meant stable transmission was constrained to Madagascar and parts of the Horn, contributing 3.5% of global PAR. Central Asia was home to 82% of global PAR with important high endemic areas coinciding with dense populations particularly in India and Myanmar. South East Asia contained areas of the highest endemicity in Indonesia and Papua New Guinea and contributed 9% of global PAR. Conclusions and Significance This detailed depiction of spatially varying endemicity is intended to contribute to a much-needed paradigm shift towards geographically stratified and evidence-based planning for P. vivax control and elimination.
Public Library of Science
Journals
2012 EN
David P. Tchouassi · Rosemary Sang · Catherine L. Sole
+3 more
In recent years, the East African region has seen an increase in arboviral diseases transmitted by blood-feeding arthropods. Effective surveillance to monitor and reduce incidence of these infections requires the use of appropriate vector sampling tools. Here, trapped skin volatiles on fur from sheep, a known preferred host of mosquito vectors of Rift Valley fever virus (RVFV), were used with a standard CDC light trap to improve catches of mosquito vectors. We tested the standard CDC light trap alone (L), and baited with (a) CO 2 (LC), (b) animal volatiles (LF), and (c) CO 2 plus animal volatiles (LCF) in two highly endemic areas for RVF in Kenya (Marigat and Ijara districts) from March–June and September–December 2010. The incidence rate ratios (IRR) that mosquito species chose traps baited with treatments (LCF, LC and LF) instead of the control (L) were estimated. Marigat was dominated by secondary vectors and host-seeking mosquitoes were 3–4 times more likely to enter LC and LCF traps [IRR = 3.1 and IRR = 3.8 respectively] than the L only trap. The LCF trap captured a greater number of mosquitoes than the LC trap (IRR = 1.23) although the difference was not significant. Analogous results were observed at Ijara, where species were dominated by key primary and primary RVFV vectors, with 1.6-, 6.5-, and 8.5-fold increases in trap captures recorded in LF, LC and LCF baited traps respectively, relative to the control. These catches all differed significantly from those trapped in L only. Further, there was a significant increase in trap captures in LCF compared to LC (IRR = 1.63). Mosquito species composition and trap counts differed between the RVF sites. However, within each site, catches differed in abundance only and no species preferences were noted in the different baited-traps. Identifying the attractive components present in these natural odors should lead to development of an effective odor-bait trapping system for population density-monitoring and result in improved RVF surveillance especially during the inter-epidemic period.
Public Library of Science
Journals
2012 EN
Bin Xu · Catherine A. Gordon · Wei Hu
+14 more
Schistosomiasis japonica is a zoonosis with a number of mammalian species acting as reservoir hosts, including water buffaloes which can contribute up to 75% to human transmission in the People's Republic of China. Determining prevalence and intensity of Schistosoma japonicum in mammalian hosts is important for calculating transmission rates and determining environmental contamination. A new procedure, the formalin–ethyl acetate sedimentation-digestion (FEA–SD) technique, for increased visualization of S. japonicum eggs in bovine feces, is described that is an effective technique for identifying and quantifying S. japonicum eggs in fecal samples from naturally infected Chinese water buffaloes and from carabao (water buffalo) in the Philippines. The procedure involves filtration, sedimentation, potassium hydroxide digestion and centrifugation steps prior to microscopy. Bulk debris, including the dense cellulosic material present in bovine feces, often obscures schistosome eggs with the result that prevalence and infection intensity based on direct visualization cannot be made accurately. This technique removes nearly 70% of debris from the fecal samples and renders the remaining debris translucent. It allows improved microscopic visualization of S. japonicum eggs and provides an accurate quantitative method for the estimation of infection in bovines and other ruminant reservoir hosts. We show that the FEA-SD technique could be of considerable value if applied as a surveillance tool for animal reservoirs of S. japonicum , particularly in areas with low to high infection intensity, or where, following control efforts, there is suspected elimination of schistosomiasis japonica.
Public Library of Science
Journals
2012 EN
Catherine B. Poole · Nathan A. Tanner · Yinhua Zhang
+2 more
In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori , as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti , Onchocerca volvulus or Dirofilaria immitis , or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia -specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis.
Public Library of Science
Journals
2012 EN
Sarah Djebali · Julien Lagarde · Philipp Kapranov
+35 more
The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.
Public Library of Science
Journals
2012 EN
JeanPierre Lavoie · Josiane Lefebvre-Lavoie · Mathilde Leclère
+4 more
Background Gene expression analyses are used to investigate signaling pathways involved in diseases. In asthma, they have been primarily derived from the analysis of bronchial biopsies harvested from mild to moderate asthmatic subjects and controls. Due to ethical considerations, there is currently limited information on the transcriptome profile of the peripheral lung tissues in asthma. Objective To identify genes contributing to chronic inflammation and remodeling in the peripheral lung tissue of horses with heaves, a naturally occurring asthma-like condition. Methods Eleven adult horses (6 heaves-affected and 5 controls) were studied while horses with heaves were in clinical remission (Pasture), and during disease exacerbation induced by a 30-day natural antigen challenge during stabling (Challenge). Large peripheral lung biopsies were obtained by thoracoscopy at both time points. Using suppression subtractive hybridization (SSH), lung cDNAs of controls (Pasture and Challenge) and asymptomatic heaves-affected horses (Pasture) were subtracted from cDNAs of horses with heaves in clinical exacerbation (Challenge). The differential expression of selected genes of interest was confirmed using quantitative PCR assay. Results Horses with heaves, but not controls, developed airway obstruction when challenged. Nine hundred and fifty cDNA clones isolated from the subtracted library were screened by dot blot array and 224 of those showing the most marked expression differences were sequenced. The gene expression pattern was confirmed by quantitative PCR in 15 of 22 selected genes. Novel genes and genes with an already defined function in asthma were identified in the subtracted cDNA library. Genes of particular interest associated with asthmatic airway inflammation and remodeling included those related to PPP3CB/NFAT, RhoA, and LTB4/GPR44 signaling pathways. Conclusions Pathways representing new possible targets for anti-inflammatory and anti-remodeling therapies for asthma were identified. The findings of genes previously associated with asthma validate this equine model for gene expression studies.
Public Library of Science
Journals
2012 EN
Isabel M. Kloumann · Christopher M. Danforth · Kameron Decker Harris
+2 more
Over the last million years, human language has emerged and evolved as afundamental instrument of social communication and semiotic representation.People use language in part to convey emotional information, leading to thecentral and contingent questions: (1) What is the emotional spectrum of naturallanguage? and (2) Are natural languages neutrally, positively, or negativelybiased? Here, we report that the human-perceived positivity of over 10,000 ofthe most frequently used English words exhibits a clear positive bias. Moredeeply, we characterize and quantify distributions of word positivity for fourlarge and distinct corpora, demonstrating that their form is broadly invariantwith respect to frequency of word use.
Public Library of Science
Journals
2012 EN
Sarah J. Moum · Catherine C. Price · Natlada Limotai
+5 more
Objective Impulse control disorders (ICDs) and dopamine dysregulation syndrome (DDS) are important behavioral problems that affect a subpopulation of patients with Parkinson's disease (PD) and typically result in markedly diminished quality of life for patients and their caregivers. We aimed to investigate the effects of subthalamic nucleus (STN) and internal globus pallidus (GPi) deep brain stimulation (DBS) on ICD/DDS frequency and dopaminergic medication usage. Methods A retrospective chart review was performed on 159 individuals who underwent unilateral or bilateral PD DBS surgery in either STN or GPi. According to published criteria, pre- and post-operative records were reviewed to categorize patients both pre- and post-operatively as having ICD, DDS, both ICD and DDS, or neither ICD nor DDS. Group differences in patient demographics, clinical presentations, levodopa equivalent dose (LED), and change in diagnosis following unilateral/bilateral by brain target (STN or GPi DBS placement) were examined. Results 28 patients met diagnostic criteria for ICD or DDS pre- or post-operatively. ICD or DDS classification did not differ by GPi or STN target stimulation. There was no change in DDS diagnosis after unilateral or bilateral stimulation. For ICD, diagnosis resolved in 2 of 7 individuals after unilateral or bilateral DBS. Post-operative development of these syndromes was significant; 17 patients developed ICD diagnoses post-operatively with 2 patients with pre-operative ICD developing DDS post-operatively. Conclusions Unilateral or bilateral DBS did not significantly treat DDS or ICD in our sample, even though a few cases of ICD resolved post-operatively. Rather, our study provides preliminary evidence that DDS and ICD diagnoses may emerge following DBS surgery.
Public Library of Science
Journals
2012 EN
Mostafa GhannadRezaie · Xing Wang · Bibhudatta Mishra
+2 more
With powerful genetics and a translucent cuticle, the Drosophila larva is an ideal model system for live imaging studies of neuronal cell biology and function. Here, we present an easy-to-use approach for high resolution live imaging in Drosophila using microfluidic chips. Two different designs allow for non-invasive and chemical-free immobilization of 3 rd instar larvae over short (up to 1 hour) and long (up to 10 hours) time periods. We utilized these ‘larva chips’ to characterize several sub-cellular responses to axotomy which occur over a range of time scales in intact, unanaesthetized animals. These include waves of calcium which are induced within seconds of axotomy, and the intracellular transport of vesicles whose rate and flux within axons changes dramatically within 3 hours of axotomy. Axonal transport halts throughout the entire distal stump, but increases in the proximal stump. These responses precede the degeneration of the distal stump and regenerative sprouting of the proximal stump, which is initiated after a 7 hour period of dormancy and is associated with a dramatic increase in F-actin dynamics. In addition to allowing for the study of axonal regeneration in vivo , the larva chips can be utilized for a wide variety of in vivo imaging applications in Drosophila .
Public Library of Science