Development and Validation of an Improved PCR Method Using the 23S-5S Intergenic Spacer for Detection of Rickettsiae in Dermacentor variabilis Ticks and Tissue Samples from Humans and Laboratory Animals

A novel nested PCR assay was developed to detect Rickettsia spp. in ticks and tissue samples from humans and laboratory animals. Primers were designed for the nested run to amplify a variable region of the 23S-5S intergenic spacer (IGS) of Rickettsia spp. The newly designed primers were evaluated using genomic DNA from 11 Rickettsia species belonging to the spotted fever, typhus, and ancestral groups and, in parallel, compared to other Rickettsia -specific PCR targets ( ompA , gltA , and the 17-kDa protein gene). The new 23S-5S IGS nested PCR assay amplified all 11 Rickettsia spp., but the assays employing other PCR targets did not. The novel nested assay was sensitive enough to detect one copy of a cloned 23S-5S IGS fragment from “ Candidatus Rickettsia amblyommii.” Subsequently, the detection efficiency of the 23S-5S IGS nested assay was compared to those of the other three assays using genomic DNA extracted from 40 adult Dermacentor variabilis ticks. The nested 23S-5S IGS assay detected Rickettsia DNA in 45% of the ticks, while the amplification rates of the other three assays ranged between 5 and 20%. The novel PCR assay was validated using clinical samples from humans and laboratory animals that were known to be infected with pathogenic species of Rickettsia . The nested 23S-5S IGS PCR assay was coupled with reverse line blot hybridization with species-specific probes for high-throughput detection and simultaneous identification of the species of Rickettsia in the ticks. “ Candidatus Rickettsia amblyommii,” R. montanensis , R. felis , and R. bellii were frequently identified species, along with some potentially novel Rickettsia strains that were closely related to R. bellii and R. conorii

Mapping of household vulnerability and identification of adaptation strategies in dryland systems of South Asia, Research Report No. 67

Low amount and high variability of rainfall in South Asian dryland production system have affected the livelihood of small and marginal households. Therefore, a marginal change in the climate could challenge the livelihood resilience of millions of farmers and affect the healthy ecosystem function in South Asia. The CGIAR Consortium Research Program on Dryland Systems (DS) focuses on DS across the world in order to tackle these problems. The overall emphasis of the research involves understanding the problem, identifying and demonstrating technologies and searching for mechanisms to promote the adoption of promising technologies. In South Asia, the program selected six districts in Andhra Pradesh (Anantapur and Kurnool), Karnataka (Bijapur) and Western Rajasthan (Jaisalmer, Barmer, and Jodhpur) as action sites..

Climate Change, Gender and Adaptation Strategies in Dryland Systems of South Asia : A Household Level Analysis in Andhra Pradesh, Karnataka and Rajasthan States of India; Research Report No. 65

There is a blossoming literature on gender and climate change issues broadly focused on the adverse effects of climate condition. These studies are mostly focused on gender inequalities in agrarian communities of developing countries where the dependence on climatic conditions for living is more apparent. Frequently, the issues of climate change, poverty, gender and economic empowerment are addressed as the most prominent in developing regions. In some cases, the studies narrow down the focus to specific weather events like droughts, floods or natural disasters in rural communities. The agrarian communities of backward areas in South Asia are some of the representative examples which are frequently presented in climate change and gender studies..

Quantification of Risk Associated with Technology Adoption in Dryland Systems of South Asia : A Household Level Analysis in Andhra Pradesh, Karnataka and Rajasthan States of India; Research Report No. 66

Climate change increasingly becomes a challenge for smallholder farmers. Strategies that will help farmers to cope with vulnerability are important. These strategies comprise a variety of interventions ranging from technical, institutional to policy. This study is an in-depth analysis of household level climate change shocks, farmers’ perception of vulnerability, adaptation strategies they followed and risk in technology adoption. A baseline survey was conducted in the dryland system action sites in three states of India: Andhra Pradesh (Kurnool and Anantapur districts); Karnataka (Bijapur district) and Rajasthan (Jaisalmer, Barmer and Jodhpur districts) in 2012-13 for 2011-12 production season. A total of 1019 farmers were surveyed..

Prevalence of Rickettsiales in ticks removed from the skin of outdoor workers in North Carolina

BackgroundTick-transmitted rickettsial diseases, such as ehrlichiosis and spotted fever rickettsiosis, are significant sources of morbidity and mortality in the southern United States. Because of their exposure in tick-infested woodlands, outdoor workers experience an increased risk of infection with tick-borne pathogens. As part of a double blind randomized-controlled field trial of the effectiveness of permethrin-treated clothing in preventing tick bites, we identified tick species removed from the skin of outdoor workers in North Carolina and tested the ticks for Rickettsiales pathogens.MethodsTicks submitted by study participants from April-September 2011 and 2012 were identified to species and life stage, and preliminarily screened for the genus Rickettsia by nested PCR targeting the 17-kDa protein gene. Rickettsia were further identified to species by PCR amplification of 23S-5S intergenic spacer (IGS) fragments combined with reverse line blot hybridization with species-specific probes and through cloning and nucleotide sequence analysis of 23S-5S amplicons. Ticks were examined for Ehrlichia and Anaplasma by nested PCR directed at the gltA, antigen-expressing gene containing a variable number of tandem repeats, 16S rRNA, and groESL genes.ResultsThe lone star tick (Amblyomma americanum) accounted for 95.0 and 92.9% of ticks submitted in 2011 (n = 423) and 2012 (n = 451), respectively. Specimens of American dog tick (Dermacentor variabilis), Gulf Coast tick (Amblyomma maculatum) and black-legged tick (Ixodes scapularis) were also identified. In both years of our study, 60.9% of ticks tested positive for 17-kDa. “Candidatus Rickettsia amblyommii”, identified in all four tick species, accounted for 90.2% (416/461) of the 23S-5S-positive samples and 52.9% (416/787) of all samples tested. Nucleotide sequence analysis of Rickettsia-specific 23S-5S IGS, ompA and gltA gene fragments indicated that ticks, principally A. americanum, contained novel species of Rickettsia. Other Rickettsiales, including Ehrlichia ewingii, E. chaffeensis, Ehrlichia sp. (Panola Mountain), and Anaplasma phagocytophilum, were infrequently identified, principally in A. americanum.ConclusionsWe conclude that in North Carolina, the most common rickettsial exposure is to R. amblyommii carried by A. americanum. Other Rickettsiales bacteria, including novel species of Rickettsia, were less frequently detected in A. americanum but are relevant to public health nevertheless.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-014-0607-2) contains supplementary material, which is available to authorized users

Fast 2D/3D object representation with growing neural gas

This work presents the design of a real-time system to model visual objects with the use of self-organising networks. The architecture of the system addresses multiple computer vision tasks such as image segmentation, optimal parameter estimation and object representation. We first develop a framework for building non-rigid shapes using the growth mechanism of the self-organising maps, and then we define an optimal number of nodes without overfitting or underfitting the network based on the knowledge obtained from information-theoretic considerations. We present experimental results for hands and faces, and we quantitatively evaluate the matching capabilities of the proposed method with the topographic product. The proposed method is easily extensible to 3D objects, as it offers similar features for efficient mesh reconstruction

Citrullination facilitates cross-reactivity of rheumatoid factor with non-IgG1 Fc epitopes in rheumatoid arthritis

Rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPAs) are the two most prevalent autoantibodies in rheumatoid arthritis (RA), and are thought to have distinct autoantigen targets. Whilst RF targets the Fc region of antibodies, ACPAs target a far broader spectrum of citrullinated peptides. Here we demonstrate significant sequence and structural homology between proposed RF target epitopes in IgG1 Fc and the ACPA target fibrinogen. Two of the three homologous sequences were susceptible to citrullination, and this modification, which occurs extensively in RA, permitted significant cross-reactivity of RF+ patient sera with fibrinogen in both western blots and ELISAs. Crucially, this reactivity was specific to RF as it was absent in RF− patient and healthy control sera, and could be inhibited by pre-incubation with IgG1 Fc. These studies establish fibrinogen as a common target for both RF and ACPAs, and suggest a new mechanism in RF-mediated autoimmune diseases wherein RF may act as a precursor from which the ACPA response evolves

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (Graduate Research Fellowship under Grant 0645960)National Institutes of Health (U.S.) (grant P01 NS055923)Pennsylvania State University. Center for Eukaryotic Gene Regulatio