Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history

Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).

Novel paradigm enables accurate monthly gestational screening to prevent congenital toxoplasmosis and more

Background

Congenital toxoplasmosis is a treatable, preventable disease, but untreated causes death, prematurity, loss of sight, cognition and motor function, and substantial costs worldwide.

Methods/Findings

In our ongoing USA feasibility/efficacy clinical trial, data collated with other ongoing and earlier published results proved high performance of an Immunochromatographic-test(ICT) that enables accurate, rapid diagnosis/treatment, establishing new paradigms for care. Overall results from patient blood and/or serum samples tested with ICT compared with gold-standard-predicate-test results found ICT performance for 4606 sera/1876 blood, 99.3%/97.5% sensitive and 98.9%/99.7% specific. However, in the clinical trial the FDA-cleared-predicate test initially caused practical, costly problems due to false-positive-IgM results. For 58 persons, 3/43 seronegative and 2/15 chronically infected persons had false positive IgM predicate tests. This caused substantial anxiety, concerns, and required costly, delayed confirmation in reference centers. Absence of false positive ICT results contributes to solutions: Lyon and Paris France and USA Reference laboratories frequently receive sera with erroneously positive local laboratory IgM results impeding patient care. Therefore, thirty-two such sera referred to Lyon's Reference laboratory were ICT-tested. We collated these with other earlier/ongoing results: 132 of 137 USA or French persons had false positive local laboratory IgM results identified correctly as negative by ICT. Five false positive ICT results in Tunisia and Marseille, France, emphasize need to confirm positive ICT results with Sabin-Feldman-Dye-test or western blot. Separate studies demonstrated high performance in detecting acute infections, meeting FDA, CLIA, WHO ASSURED, CEMark criteria and patient and physician satisfaction with monthly-gestational-ICT-screening.

Conclusions/Significance

This novel paradigm using ICT identifies likely false positives or raises suspicion that a result is truly positive, rapidly needing prompt follow up and treatment. Thus, ICT enables well-accepted gestational screening programs that facilitate rapid treatment saving lives, sight, cognition and motor function. This reduces anxiety, delays, work, and cost at point-of-care and clinical laboratories.

Author’s Summary

Toxoplasmosis is a major health burden for developed and developing countries, causing damage to eyes and brain, loss of life and substantial societal costs. Prompt diagnosis in gestational screening programs enables treatment, thereby relieving suffering, and leading to > 14-fold cost savings for care. Herein, we demonstrate that using an ICT that meets WHO ASSURED-criteria identifying persons with/without antibody to Toxoplasma gondii in sera and whole blood with high sensitivity and specificity, is feasible to use in USA clinical practice. We find this new approach can help to obviate the problem of detection of false positive anti- T.gondii IgM results for those without IgG antibodies to T.gondii when this occurs in present, standard of care, predicate USA FDA cleared available assays. Thus, this accurate test facilitates gestational screening programs and a global initiative to diagnose and thereby prevent and treat T.gondii infection. This minimizes likelihood of false positives (IgG and/or IgM) while maintaining maximum sensitivity. When isolated IgM antibodies are detected, it is necessary to confirm and when indicated continue follow up testing in ∼2 weeks to establish seroconversion. Presence of a positive ICT makes it likely that IgM is truly positive and a negative ICT makes it likely that IgM will be a false positive without infection. These results create a new, enthusiastically-accepted, precise paradigm for rapid diagnosis and validation of results with a second-line test. This helps eliminate alarm and anxiety about false-positive results, while expediting needed treatment for true positive results and providing back up distinguishing false positive tests.

Molecular epidemiology of the citrus bacterial pathogen Xanthomonas citri pv. citri from the Arabian Peninsula reveals a complex structure of specialist and generalist strains

Molecular epidemiology studies are essential to refine our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence, and to understand the factors that shape their population structure. Microsatellite and minisatellite typing are useful techniques for deciphering the population structure of Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker. This paper presents a molecular epidemiology study, which has improved our understanding of the history of the pathogen's introductions into the Arabian Peninsula, since it was first reported in the 1980s. An unexpectedly high genetic diversity of the pathogen was revealed. The four distinct genetic lineages within X. citri pv. citri, which have been reported throughout the world, were identified in the Arabian Peninsula, most likely as the result of multiple introductions. No copper‐resistant X. citri pv. citri strains were identified. The pathogen's population structure on Mexican lime (their shared host species) was closely examined in two countries, Saudi Arabia and Yemen. We highlighted the marked prevalence of specialist pathotype A* strains in both countries, which suggests that specialist strains of X. citri pv. citri may perform better than generalist strains when they occur concomitantly in this environment. Subclade 4.2 was the prevailing lineage identified. Several analyses (genetic structure deciphered by discriminant analysis of principal components, R_ST‐based genetic differentiation, geographic structure) congruently suggested the role of human activities in the pathogen's spread. We discuss the implications of these results on the management of Asiatic citrus canker in the region.

First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

Diversity and Geographical Structure of Xanthomonas citri pv. citri on Citrus in the South West Indian Ocean Region

A thorough knowledge of genotypic and phenotypic variations (e.g., virulence, resistance to antimicrobial compounds) in bacteria causing plant disease outbreaks is key for optimizing disease surveillance and management. Using a comprehensive strain collection, tandem repeat-based genotyping techniques and pathogenicity assays, we characterized the diversity of X. citri pv. citri from the South West Indian Ocean (SWIO) region. Most strains belonged to the prevalent lineage 1 pathotype A that has a wide host range among rutaceous species. We report the first occurrence of genetically unrelated, nonepidemic lineage 4 pathotype A* (strains with a host range restricted to Mexican lime and related species) in Mauritius, Moheli and Réunion. Microsatellite data revealed that strains from the Seychelles were diverse, grouped in three different clusters not detected in the Comoros and the Mascarenes. Pathogenicity data suggested a higher aggressiveness of strains of one of these clusters on citron (Citrus medica). With the noticeable exception of the Comoros, there was no sign of recent interisland movement of the pathogen. Consistent with this finding, the copL gene, a marker for the plasmid-borne copLAB copper resistance that was recently identified in Réunion, was not detected in 568 strains from any islands in the SWIO region apart from Réunion.

Quantitation of Tebuconazole in Liquid and Solid Formulations by Capillary GC: Collaborative Study

A capillary gas chromatographic method has been developed for quantitation of tebuconazole (Folicur, Elite, Raxil, Lynx) in liquid and solid formulations. Tebuconazole is a broad-spectrum, systemic foliar fungicide used to control diseases of wheat, barley, peanut, and grasses grown for seed. Samples are dissolved in acetone and analyzed by capillary gas chromatography (GC) with dicyclohexyl phthalate as internal standard. Twenty-two laboratories from 11 countries participated in a collaborative study of the method. Each collaborator was provided reference standard, internal standard, and blind duplicate samples from 6 formulations: aqueous flowable (F), aqueous emulsifiable concentrate (EW), emulsifiable concentrate for seed treatment (ES), flowable for seed treatment (FS), wettable powder (WP), and dry flowable (DF). Collaborators were instructed to use peak area measurements for quantitation. The seed treatment flowable formulation required confirmation of accurate integration values by the collaborator. Relative standard deviation values for reproducibility (RSDR) for analysis of the formulations were as follows: 3.6 lb/gal F, 1.22; 250 g/L EW, 1.13; 15 g/L ES, 2.40; 25 g/L FS, 2.65; 25% WP, 0.96; 25% DF, 0.72; 45% DF, 0.72. The capillary GC method for quantitation of tebuconazole in fungicide formulations has been adopted first action by AOAC INTERNATIONAL.

Hot Rocks and Not-So-Hot Rocks on the Seashore: Patterns and Body-Size Dependent Consequences of Microclimatic Variation in Intertidal Zone Boulder Habitat

Microclimatic variation has emerged as an important driver of many ecological and evolutionary processes. Nonetheless, fine-scale temperature data are still rare in most habitats, limiting our ability to understand the consequences of microclimatic variation under current and future conditions. We measured fine-scale thermal variation in a common, species-rich, but rarely studied habitat with respect to temperature: the airspaces under rocks on intertidal zone boulder shores. The effects of thermal variation were investigated using physiological, behavioral, and demographic responses of the porcelain crab Petrolisthes cinctipes. Habitat temperatures were measured at fine spatial and temporal resolution over 18 months, producing 424,426 temperature records. Microclimatic variation increased with increasing intertidal elevation, particularly with respect to heat extremes. However, mean temperatures were similar across the entire intertidal zone. Overheating risk for P. cinctipes increases with intertidal elevation but is size dependent, as large animals are more heat sensitive than small animals. Still, microclimatic variation high in the intertidal zone provided thermal refugia even under the warmest conditions. Size-dependent thermal responses predicted that large crabs should be rare high in the intertidal zone, which was supported by demographic data. Furthermore, simulations parameterized by our microclimate and organismal data recapitulated demographic patterns. Therefore, interactions between microclimatic variation and size-dependent thermal responses may have significant ecological repercussions that warrant greater attention.

Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity

Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv. citri, a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv. citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies.

Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements

Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper-resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain dependent with the novel identification in X. citri pv. citri of copABCD and a cus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. This indicates the system's great versatility. The mining of all available bacterial genomes suggested that, within the bacterial community, the spread of copper resistance associated with mobile elements and their plasmid environments was primarily restricted to the Xanthomonadaceae family.

Multilocus Variable Number of Tandem Repeat Analysis Reveals Multiple Introductions in Spain of Xanthomonas arboricola pv. pruni, the Causal Agent of Bacterial Spot Disease of Stone Fruits and Almond

Xanthomonas arboricola pv. pruni is the causal agent of the bacterial spot disease of stone fruits, almond and some ornamental Prunus species. In Spain it was first detected in 2002 and since then, several outbreaks have occurred in different regions affecting mainly Japanese plum, peach and almond, both in commercial orchards and nurseries. As the origin of the introduction(s) was unknown, we have assessed the genetic diversity of 239 X. arboricola pv. pruni strains collected from 11 Spanish provinces from 2002 to 2013 and 25 reference strains from international collections. We have developed an optimized multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 18 microsatellites and five minisatellites. A high discriminatory power was achieved since almost 50% of the Spanish strains were distinguishable, confirming the usefulness of this genotyping technique at small spatio-temporal scales. Spanish strains grouped in 18 genetic clusters (conservatively delineated so that each cluster contained haplotype networks linked by up to quadruple-locus variations). Furthermore, pairwise comparisons among populations from different provinces showed a strong genetic differentiation. Our results suggest multiple introductions of this pathogen in Spain and redistribution through contaminated nursery propagative plant material.

Natural Infection of Cashew (Anacardium occidentale) by Xanthomonas citri pv. mangiferaeindicae in Burkina Faso

Xanthomonas citri pv. mangiferaeindicae is the causal agent of bacterial canker of mango (Mangifera indica, Anacardiaceae), a disease of international importance. Since the original description of the bacterium in the 1940s, the status of cashew (Anacardium occidentale, Anacardiaceae) as a host species has been unclear. Here, we report the first outbreak of a cashew bacterial disease in Burkina Faso (Western Africa) where X. citri pv. mangiferaeindicae recently emerged on mango. A comprehensive molecular characterization, based on multilocus sequence analysis, supplemented with pathogenicity assays of isolates obtained during the outbreak, indicated that the causal agent on cashew in Burkina Faso is X. citri pv. mangiferaeindicae and not X. citri pv. anacardii, which was previously reported as the causal agent of a cashew bacterial leaf spot in Brazil. Pathogenicity data supported by population biology in Burkina Faso suggest a lack of host specialization. Therefore, the inoculum from each crop is potentially harmful to both host species. Symptoms induced on cashew leaves and fruit by X. citri pv. mangiferaeindicae and nonpigmented strains of X. citri pv. anacardii are similar, although the causative bacteria are genetically different. Thus, xanthomonads pathogenic on cashew may represent a new example of pathological convergence in this bacterial genus.

First Report of Xanthomonas citri pv. mangiferaeindicae Causing Mango Bacterial Canker on Mangifera indica in Ivory Coast

Xanthomonas citri pv. mangiferaeindicae causing bacterial canker (or black spot) is a major mango (Mangifera indica L.) pathogen in tropical and subtropical areas (3). The bacterium infects a wide range of mango cultivars, and induces raised, angular, black leaf lesions, sometimes with a yellow chlorotic halo. Fruit symptoms first appear as small water-soaked spots on the lenticels turning into star-shaped, erumpent lesions, which exude an infectious gum, yielding tear-stain patterns. Severe infections cause severe defoliation and/or premature fruit drop. Twig cankers are potential sources of inoculum and weaken branch resistance to winds. Drastic yield losses have been reported at grove scale for susceptible cultivars (3). Mango leaves showing typical angular, black, raised leaf lesions were first observed and collected in April 2014 from trees cv. Kent in five localities of the Korhogo province of Ivory Coast (i.e., the major commercial mango-growing area in this country). Non-pigmented Xanthomonas-like colonies were isolated on KC semi-selective medium (4). Five strains (LL60-1, LL61-1, LL62-1, LL63-1, and LL64-1), one from each locality, were compared by multilocus sequence analysis (MLSA) to the type strain of X. citri and the pathotype strain of several X. citri pathovars, including pvs. anacardii and mangiferaeindicae. This assay targeted the atpD, dnaK, efp, and gyrB genes, as described previously (2). Nucleotide sequences were 100% identical to those of the pathotype strain of X. citri pv. mangiferaeindicae whatever the gene assayed, but differed from any other assayed X. citri pathovar. Leaves of mango cv. Maison Rouge from the youngest vegetative flush were infiltrated (10 inoculation sites/leaf for three replicate leaves on different plants/bacterial strain) as detailed previously (1) with the same five strains. Bacterial suspensions (~1 × 10⁵ cfu/ml) were prepared in 10 mM Tris buffer (pH 7.2) from 16-h-old cultures on YPGA (7 g yeast, 7 g peptone, 7 g glucose, and 18 g agar/liter, pH 7.2). The negative control treatment consisted of three leaves infiltrated with sterile Tris buffer (10 sites/leaf). Plants were incubated in a growth chamber at 30 ± 1°C by day and 26 ± 1°C by night (12-h day/night cycle) at 80 ± 5% RH. All leaves inoculated with the strains from Ivory Coast showed typical symptoms of bacterial canker a week after inoculation. No lesions were recorded from the negative controls. The pathogen was recovered at high population densities (>1 × 10⁶ cfu/lesion) from leaf lesions, typical of a compatible interaction (1) and isolated colonies were identified as the target by atpD sequencing (2). Koch's postulates have therefore been fully verified. This is the first report of the disease in Ivory Coast, a country which has been an internationally significant mango exporter (up to 15,000 tons per year) over the last two decades. A high disease incidence and severity were observed, outlining the need for implementing integrated pest management in mango groves and the production of disease-free nursery stock. This report further expands the distribution of the pathogen in West Africa after its first description from Ghana in 2011 (5) and subsequently in other neighboring countries. References: (1) N. Ah-You et al. Phytopathology 97:1568, 2007. (2) L. Bui Thi Ngoc et al. Int. J. Syst. Evol. Microbiol. 60:515, 2010. (3) L. Gagnevin and O. Pruvost. Plant Dis. 85:928, 2001. (4) O. Pruvost et al. J. Appl. Microbiol. 99:803, 2005. (5) O. Pruvost et al. Plant Dis. 95:774, 2011.

First Report of Xanthomonas citri pv. citri Pathotype A Causing Asiatic Citrus Canker in Grande Comore and Anjouan

The causal agent of Asiatic citrus canker, Xanthomonas citri pv. citri, is a bacterium of major economic importance in tropical and subtropical citrus-producing areas. X. citri pv. citri pathotype A can cause severe infection in a wide range of citrus species and induces erumpent, callus-like lesions with water-soaked margins evolving to corky cankers and leading to premature fruit, leaf drop, and twig dieback on susceptible cultivars. This quarantine organism can strongly impact citrus markets so it has consequently been subjected to eradication efforts and international quarantine regulations. Asiatic citrus canker occurs on most islands in the Southwest Indian Ocean region including the Mascarene and Seychelles archipelagos. In the Comoros archipelago, the disease was observed for the first time in Mohéli island in 1966 (2), but had not yet been reported in neighboring islands, Grande Comore and Anjouan. In September 2013, leaves of key lime (Citrus aurantifolia) and sweet orange (C. sinensis) showing symptoms of citrus canker were collected from Anjouan, Grande Comore, and Mohéli. Nine Xanthomonas-like strains (three from each of the three islands) were isolated using KC semi-selective medium (5) from diseased samples (LK126-3, LK127-7, LK128-2, LK131-10, LK137-1, LK141-3, LK144-5, LK145-5, LK146-2). Based on a specific PCR assay with 4/7 primers (4), all Xanthomonas-like strains were tentatively identified as X. citri pv. citri. All strains produced a 468-bp amplicon similar to X. citri pv. citri strain IAPAR 306 used as a positive control. Negative control reactions with sterile tris buffer did not produce amplicons. Multilocus sequence analysis (MLSA) targeting six housekeeping genes (atpD, dnaK, efp, gltA, gyrB, and lepA) (1,3) fully identified all strains from the Comoros as X. citri pv. citri. More specifically, eight strains were identified as sequence type ST2 composed of pathotype A strains of X. citri pv. citri (3) (including all strains from the Southwest Indian Ocean region) while one of them (LK141-3 from Mohéli) was identified as a new sequence type based on a non-synonymous single nucleotide polymorphism in gyrB (accession KJ941208). All strains were inoculated by a detached leaf assay (3) onto Mexican lime SRA 140 (C. aurantifolia), Tahiti lime SRA 58 (C. latifolia), sweet orange New Hall Navel SRA 343 (C. sinensis), grapefruit Henderson SRA 336 (C. paradisi), and Ortanique tangor SRA 110 (C. reticulata × C. sinensis). All citrus species inoculated produced typical erumpent, callus-like tissue at wound sites. Xanthomonas-like yellow colonies were re-isolated from lesions produced on Mexican lime. Boiled bacterial suspensions were assayed by PCR with 4/7 primers (4) and produced the expected amplicon, fulfilling Koch's postulates. No lesions developed on the negative control consisting of inoculations with sterile tris buffer. This is the first report of X. citri pv. citri-A causing Asiatic citrus canker in Grande Comore and Anjouan islands confirming the wide distribution of the pathogen in Southwest Indian Ocean islands. Canker-free nurseries and grove sanitation should be implemented to decrease the prevalence of Asiatic canker in the Comoros. References: (1) N. F. Almeida et al. Phytopathology 100:208, 2010. (2) J. Brun. Fruits 26:533, 1971. (3) L. Bui Thi Ngoc et al. Int. J. Syst. Evol. Microbiol. 60:515, 2010. (4) J. S. Hartung et al. Phytopathology 86:95, 1996. (5) O. Pruvost et al. J. Appl. Microbiol. 99:803, 2005.

A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage

MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).

Predictive-focus illumination for reducing photodamage in live-cell microscopy

Due to photobleaching and phototoxicity induced by high-intensity excitation light, the number of fluorescence images that can be obtained in live cells is always limited. This limitation becomes particularly prominent in multidimensional recordings when multiple Z-planes are captured at every time point. Here we present a simple technique, termed predictive-focus illumination (PFI), which helps to minimize cells' exposure to light by decreasing the number of Z-planes that need to be captured in live-cell 3D time-lapse recordings. PFI utilizes computer tracking to predict positions of objects of interest (OOIs) and restricts image acquisition to small dynamic Z-regions centred on each OOI. Importantly, PFI does not require hardware modifications and it can be easily implemented on standard wide-field and spinning-disc confocal microscopes.

Evidence for associations between the purinergic receptor P2X(7) (P2RX7) and toxoplasmosis

Congenital Toxoplasma gondii infection can result in intracranial calcification, hydrocephalus, and retinochoroiditis. Acquired infection is commonly associated with ocular disease. Pathology is characterized by strong pro-inflammatory responses. Ligation of ATP by purinergic receptor P2X₇, encoded by P2RX7, stimulates pro-inflammatory cytokines and can lead directly to killing of intracellular pathogens. To determine whether P2X₇ plays a role in susceptibility to congenital toxoplasmosis, we examined polymorphisms at P2RX7 in 149 child/parent trios from North America. We found association (FBAT Z scores ±2.429; P= 0.015) between the derived C(+)G(−) allele (f= 0.68; OR= 2.06; 95% CI: 1.14–3.75) at SNP rs1718119 (1068T>C; Thr-348-Ala), and a second synonymous variant rs1621388 in linkage disequilibrium with it, and clinical signs of disease per se. Analysis of clinical sub-groups showed no association with hydrocephalus, with effect sizes for associations with retinal disease and brain calcifications enhanced (OR=3.0 to 4.25; 0.004<P<0.009) when hydrocephalus was removed from the analysis. Association with toxoplasmic retinochoroiditis was replicated (FBAT Z scores ±3.089; P= 0.002) in a small family-based study (60 families; 68 affected offspring) of acquired infection in Brazil, where the ancestral T(+) allele (f= 0.296) at SNP rs1718119 was strongly protective (OR= 0.27; 95% CI: 0.09–0.80). (Words 194)

Long-term proton pump inhibitor use in children: a retrospective review of safety

The objective of this work was to assess the efficacy of continuous proton pump inhibitor (PPI) therapy in children and to evaluate changes in biochemical, endoscopic, and histologic parameters during such treatment. A retrospective review of children receiving PPI therapy continuously for 1 year or more with baseline and follow-up esophageal and gastric biopsies on treatment was conducted to assess type, frequency, and duration of PPI dosing, symptom relief, gastrin levels, histologic findings, and adverse events. A total of 113 children (59 male, median age 4.5 years) were identified. Of these, 31% (35/113) were neurologically impaired. The median treatment duration was 35.2 months. Elevated serum gastrin levels occurred in 73% of children with no statistically significant differences in gastrin level by PPI type, dose, and dosing frequency or treatment duration. Adverse events were reported by 12% of children: diarrhea (5%) and constipation (4%) were the most frequent. Long-term PPI therapy appears to be effective, safe and well tolerated in children despite some biochemical, endoscopic, and histologic changes.

Adult Papillary Renal Tumor With Oncocytic Cells

We report a series of 10 oncocytic renal papillary tumors, with the aim of determining their clinicopathologic features. All patients were male (median age, 71 years), treated by radical nephrectomy and free of recurrence or metastasis (median follow-up, 62 months). Tumors (median size, 3.3 cm) were intrarenal and well limited, with no extrarenal extension. They consisted of thin, nonfibrotic papillae lined by a single layer of oncocytic cells, with finely granular eosinophilic cytoplasm and round regular nucleus exhibiting central nucleolus (Fuhrman grade II, except for one grade III). Foci of necrosis were present in most cases. All tumors were immunoreactive for alpha-methylacyl-coenzyme A racemase, vimentin, and CD10; 4 expressed renal cell carcinoma antigen and 3 cytokeratin 7. There were a low number of cytogenetic changes in the 5 analyzed cases (median, 4; range, 1-7), with no trisomy 7 or 17. Papillary architecture, necrosis, and immunohistochemical profiles argued against the diagnosis of oncocytoma and suggested our cases to be part of the papillary renal cell carcinoma group. However, the cases were atypical for type 1 papillary carcinoma (due to oncocytic cells and absence of trisomy 17) and for type 2 (due to a good outcome). These results suggest that adult papillary renal tumors with oncocytic cells might be a distinct variant in the papillary renal cell carcinoma group.

Modeling of clusters in a strong 248-nm laser field by a three-dimensional relativistic molecular dynamic model

A relativistic time-dependent three-dimensional particle simulation model has been developed to study the interaction of intense ultrashort KrF (248 nm) laser pulses with small Xe clusters. The trajectories of the electrons and ions are treated classically according to the relativistic equation of motion. The model has been applied to a different regime of ultrahigh intensities extending to 10(21) W/ cm(2). In particular, the behavior of the interaction with the clusters from intensities of approximately 10(15) W/cm(2) to intensities sufficient for a transition to the so-called "collective oscillation model" has been explored. At peak intensities below 10(20) W/cm(2), all electrons are removed from the cluster and form a plasma. It is found that the "collective oscillation model" commences at intensities in excess of 10(20) W/cm(2), the range that can be reached in stable relativistic channels. At these high intensities, the magnetic field has a profound effect on the shape and trajectory of the electron cloud. Specifically, the electrons are accelerated to relativistic velocities with energies exceeding 1 MeV in the direction of laser propagation and the magnetic field distorts the shape of the electron cloud to give the form of a pancake.

Retinal thickness measurements from optical coherence tomography using a Markov boundary model

We present a system for detecting retinal boundaries in optical coherence tomography (OCT) B-scans. OCT is a relatively new imaging modality giving cross-sectional images that are qualitatively similar to ultrasound. However, the axial resolution with OCT is much higher, on the order of 10 microm. Objective, quantitative measures of retinal thickness may be made from OCT images. Knowledge of retinal thickness is important in the evaluation and treatment of many ocular diseases. The boundary-detection system presented here uses a one-dimensional edge-detection kernel to yield edge primitives. These edge primitives are rated, selected, and organized to form a coherent boundary structure by use of a Markov model of retinal boundaries as detected by OCT. Qualitatively, the boundaries detected by the automated system generally agreed extremely well with the true retinal structure for the vast majority of OCT images. Only one of the 1450 evaluation images caused the algorithm to fail. A quantitative evaluation of the retinal boundaries was performed as well, using the clinical application of automatic retinal thickness determination. Retinal thickness measurements derived from the algorithm's results were compared with thickness measurements from manually corrected boundaries for 1450 test images. The algorithm's thickness measurements over a 1-mm region near the fovea differed from the corrected thickness measurements by less than 10 microm for 74% of the images and by less than 25 microm (10% of normal retinal thickness) for 98.4% of the images. These errors are near the machine's resolution limit and still well below clinical significance. Current, standard clinical practice involves a qualitative, visual assessment of retinal thickness. A robust, quantitatively accurate system such as ours can be expected to improve patient care.

Stable relativistic/charge-displacement channels in ultrahigh power density (approximately 10(21 W/cm3) plasmas

Robust stability is a chief characteristic of relativistic/charge-displacement self-channeling. Theoretical analysis of the dynamics of this stability (i) reveals a leading role for the eigenmodes in the development of stable channels, (ii) suggests a technique using a simple longitudinal gradient in the electron density to extend the zone of stability into the high electron density/high power density regime, (iii) indicates that a situation approaching unconditional stability can be achieved, (iv) demonstrates the efficacy of the stable dynamics in trapping severely perturbed beams in single uniform channels, and (v) predicts that approximately 10(4) critical powers can be trapped in a single stable channel. The scaling of the maximum power density with the propagating wavelength lambda is shown to be proportional to lambda-4 for a given propagating power and a fixed ratio of the electron plasma density to the critical plasma density. An estimate of the maximum power density that can be achieved in these channels with a power of approximately 2 TW at a UV (248 nm) wavelength gives a value of approximately 10(21) W/cm3 with a corresponding atomic specific magnitude of approximately 60 W/atom. The characteristic intensity propagating in the channel under these conditions exceeds 10(21) W/cm2.

Characteristics of patients receiving or foregoing resuscitation at the time of cardiopulmonary arrest

OBJECTIVE

To compare clinical, functional and social characteristics of DNR patients at the time of their cardiopulmonary arrest with characteristics of patients who receive cardiopulmonary resuscitation.

DESIGN

Retrospective chart review of all 261 patients who had a cardiopulmonary arrest during a 6-month period in an academic institution.

SETTING

Teaching Veterans Affairs Medical Center serving a large metropolitan area.

MEASUREMENTS

Demographic characteristics, medical diagnoses, and measures of functional status were collected when DNR orders were initiated and at the time of cardiopulmonary arrest.

RESULTS

The mean age of the studied group was 62 years. Ninety-nine percent were males, and the majority were non-Hispanic white men. One hundred ninety-eight (76%) patients/proxies elected for limiting treatment. Most (85%) elected a DNR order only. Patients were the most frequently documented participants in advance directive decisions in the DNR group. At the time of cardiopulmonary arrest, a higher proportion of the CPR group had coronary artery disease or chronic renal failure, and a higher proportion of the DNR group had cancer or AIDS. The functional status of the DNR group deteriorated from the time of DNR order to death. At the time of cardiopulmonary arrest, the majority of both groups were dependent in all functional domains, and 70% of the DNR group were stuporous or comatose compared with 47% of the CPR group (P = .05). DNR patients were hospitalized for an average of 13.7 +/- 29.5 days after a DNR order was initiated. Six of the 81 patients who received CPR (7.4%) were alive at discharge.

CONCLUSIONS

Patients and physicians deciding to implement a DNR order may be overly focused on medical diagnoses and less so on functional status. A significant proportion of patients with clinical characteristics associated with poor CPR outcome are electing for CPR.

Measurement of 160-fs, 248-nm pulses by two-photon fluorescence in fused-silica crystals

Measurements of 160-fs, 248-nm ultrashort pulses are obtained through a two-photon fluorescence measurement based on the two-photon-induced color-center fluorescence in fused-silica crystals. The method proved to be reliable and advantageous in comparison with two-photon fluorescence techniques employing other materials, both solid state and gaseous.

Congenital toxoplasmosis transmitted from an immunologically competent mother infected before conception

Congenital transmission of Toxoplasma gondii from a mother who was apparently immunologically competent and who had toxoplasmic lymphadenitis 2 months before conception is described. Since no T. gondii-specific serological data were available for this mother from the time her lymph node biopsy specimen was obtained, the specimen was studied by polymerase chain reaction (PCR) to determine whether the T. gondii B1 gene was present. The predictive diagnostic value of histologic findings previously considered to be classic signs of T. gondii lymphadenitis also was studied. This was done by correlation of serological tests diagnostic of acute acquired T. gondii infection and presence of characteristic findings in biopsy specimens from persons without known immunocompromise. Both PCR and review of the characteristic features of her lymph node biopsy specimen confirmed the diagnosis of preconceptual infection in the mother. We also discuss two other cases in which apparently immunologically competent mothers with preconceptually acquired infection transmitted this parasite to their fetuses.

Biomedical three-dimensional holographic microimaging at visible, ultraviolet and X-ray wavelengths

A new imaging technology is under advanced development that has several key advantages over conventional forms of microimaging performed with standard light microscopes, confocal light microscopes, and electron microscopes. The image created by this microscope possesses several unique features: It is intrinsically three-dimensional; it can be formed with very high contrast, a characteristic of the phase-sensitive nature of the recording; the information contained in the image is obtained in a single exposure of the specimen, a feature that eliminates the accumulation of damage to living systems that can occur with techniques utilizing multiple exposures; the method of image construction is fundamentally free from aberration (distortion), thereby obviating the need to employ complex procedures for correction; the exact focal plane of any optical section is digitally determined through computation and is not based on any mechanical adjustments; and the principles of operation, including the computational processes and modalities of image presentation, are uniform over the full range of spectral coverage spanning from the visible (approximately 500 nm) to the X-ray (approximately 0.3 nm) regions. The application of this new technology is expected to open new cost-effective avenues to the understanding, prevention and treatment of broad areas of human disease.

Young children's performance on a task sensitive to the memory functions of the medial temporal lobe in adults--the delayed nonmatching-to-sample task--reveals problems that are due to non-memory-related task demands

Delayed nonmatching-to-sample performance was examined in children and found to be poor from 12 months until almost 2 years even at 5-s delay, although 5 s is well within such children's memory capacity. After 12 months of age, performance did not differ by delay (5 or 30 s). Because children's problems seemed largely unrelated to the task's memory demands, the 2 final studies explored the role of other cognitive abilities (deduction of an abstract rule, speed of processing, and resistance to interference or distraction). Telling children the rule or quadrupling sample presentation time had little effect. Because a salient stimulus (the reward) might interfere with keeping one's attention on the sample, the reward was omitted during initial sample presentation. This helped; at the 5-s delay, 15-month-olds performed at least as well as 21-month-olds in the basic condition, and 12-month-olds performed almost as well. Implications for the cognitive abilities improving during the 2nd year and for the functions of the medial temporal lobe are discussed.

Congenital toxoplasmosis. The Toxoplasmosis Study Group

Congenital toxoplasmosis is a preventable and treatable disease with predominant neurological and ophthalmologic manifestations. These manifestations and approaches to diagnosis, treatment, and prevention of this infection are considered. Outcomes with and without treatment are emphasized. The following also are discussed: recent advances in understanding the organism; its life cycle, epidemiology, pathogenesis, and pathology; and areas in which improvements in diagnosis, treatment, and prevention are needed.

Young children's performance on a task sensitive to the memory functions of the medial temporal lobe in adults--the delayed nonmatching-to-sample task--reveals problems that are due to non-memory-related task demands

Delayed nonmatching-to-sample performance was examined in children and found to be poor from 12 months until almost 2 years even at 5-s delay, although 5 s is well within such children's memory capacity. After 12 months of age, performance did not differ by delay (5 or 30 s). Because children's problems seemed largely unrelated to the task's memory demands, the 2 final studies explored the role of other cognitive abilities (deduction of an abstract rule, speed of processing, and resistance to interference or distraction). Telling children the rule or quadrupling sample presentation time had little effect. Because a salient stimulus (the reward) might interfere with keeping one's attention on the sample, the reward was omitted during initial sample presentation. This helped; at the 5-s delay, 15-month-olds performed at least as well as 21-month-olds in the basic condition, and 12-month-olds performed almost as well. Implications for the cognitive abilities improving during the 2nd year and for the functions of the medial temporal lobe are discussed.

Fourier-transform holographic microscope

We describe a holographic microscope with a spatial resolution approaching the diffraction limit. The instrument uses a tiny drop of glycerol as a lens to create the spherically diverging reference illumination necessary for Fourier-transform holography. Measurement of the point-spread function, which is obtained by imaging a knife edge in dark-field illumination, indicates a transverse resolution of 1.4 microm with wavelength lambda = 514.5 nm. Longitudinal resolution is obtained from the holograms by the numerical equivalent of optical sectioning. We describe the method of reconstruction and demonstrate the microscope's capability with selected biological specimens. The instrument offers two unique capabilities: (1) it can collect three-dimensional information in a single pulse of light, avoiding specimen damage and bleaching; and (2) it can record three-dimensional motion pictures from a series of light pulses. The conceptual design is applicable to a broad range of wavelengths and we discuss extension to the x-ray regime.

Method of concentration of power in materials for x-ray amplification

Recent experimental and theoretical results indicate that a new technique for the controlled concentration of power in materials may be feasible. The power levels that are potentially achievable are sufficient for the generation of amplification of x-ray wavelengths in the kilovolt range. The method of power concentration involves the combination of (1) a new ultrahigh brightness subpicosecond laser technology, (2) multiphoton coupling to atoms and molecules, and (3) a new channeled mode of electromagnetic propagation. The energy scaling of this approach is the most important consideration, and it is shown that the control of the propagation is the key factor that enables high levels of amplification in the kilovolt regime to be achieved with a total excitation energy of ~1 J.

Levels of pyrimethamine in sera and cerebrospinal and ventricular fluids from infants treated for congenital toxoplasmosis. Toxoplasmosis Study Group

Pyrimethamine levels in sera, cerebrospinal fluid (CSF), and ventricular fluid were measured by using reversed-phase high-pressure liquid chromatography. The specimens were from 37 infants receiving pyrimethamine for treatment of suspect or proven congenital toxoplasmosis. Pyrimethamine half-life in serum was 64 +/- 12 h when determined by study of terminal-phase kinetics of samples obtained from nine babies. This half-life was significantly different (P = 0.008) from the pyrimethamine half-life (33 +/- 12 h) determined by terminal-phase kinetics for two babies of the same age taking phenobarbital. Serum pyrimethamine levels at various intervals after dosages of pyrimethamine were also lower for infants receiving phenobarbital. Levels measured in sera from babies taking the same dose of pyrimethamine throughout their first year of life did not appear to vary significantly over time or at different ages (P greater than 0.05). Mean +/- standard deviation serum levels 4 h after a pyrimethamine dose were 1.297 +/- 0.54 micrograms/ml for babies taking 1 mg of pyrimethamine per kg of body weight daily and 0.7 +/- 0.26 microgram/ml for babies taking 1 mg/kg each Monday, Wednesday, and Friday. Levels in CSF were approximately 10 to 25% of concomitant levels in serum. Serum folate levels for infants who took 0.64 to 1.7 mg leukovorin per kg ranged from 33 to 663 ng/ml. To determine whether the levels of pyrimethamine in serum and CSF of treated infants were in a range that affected the most virulent, rapidly replicating, and standard laboratory strain of Toxoplasma gondii, effects of various concentrations of pyrimethamine and sulfadiazine on replication of T. gondii in vitro were assessed. The levels of the antimicrobial agents effective in vitro were in the range of levels of pyrimethamine achieved in sera and CSF. Although folinic acid could inhibit the therapeutic effect of pyrimethamine and sulfadiazine in vitro, inhibition was noted only at levels (> or = 4,800 ng/ml) that were considerably higher than the folate levels found in the treated infants' sera.

Absence of sensorineural hearing loss in treated infants and children with congenital toxoplasmosis

Educationally significant hearing loss has been reported in 10% to 15% of children with congenital toxoplasmosis. As part of a pilot study to assess feasibility and safety of prolonged therapy for congenital toxoplasmosis, 30 congenitally infected infants and children were evaluated for auditory function. Serial testing, beginning within 2 months of birth, was performed. Availability of auditory brainstem response (ABR) testing made evaluation at an earlier age than previously possible. Six (20%) of the 30 infants had mild to moderate conductive type hearing loss associated with otitis media. No infant or child had sensorineural hearing loss. The better outcome we observed compared to previous reports of a 15% to 26% incidence of sensorineural hearing loss and 10% to 15% incidence of educationally significant, bilateral hearing impairment may be related to early initiation and/or prolonged institution of antimicrobial therapy. Continued followup to exclude progressive hearing impairment and study of larger numbers of children are needed to verify these preliminary findings.

Plasma production from ultraviolet-transmitting targets using subpicosecond ultraviolet radiation

Plasma produced from ultraviolet-transmitting solid targets undergoing intense (>10(16) W/cm(2)) subpicosecond (~600 fs) ultraviolet (248 nm) irradiation have been studied under conditions for which no interfering prepulse plasma is generated. Time and spatially integrated measurements of the x-ray emission for H-like and He-like Mg and Si were found to be consistent with LASNEX calculations that model the laser-target interaction.