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1.  Correlation of multiple sclerosis (MS) incidence trends with solar and geomagnetic indices: Time to revise the method of reporting MS epidemiological data 
Iranian Journal of Neurology  2014;13(2):64-69.
Background: Recently, we introduced solar related geomagnetic disturbances (GMD) as a potential environmental risk factor for multiple sclerosis (MS). The aim of this study was to test probable correlation between solar activities and GMD with long-term variations of MS incidence.
Methods: After a systematic review, we studied the association betwee
n alterations in the solar wind velocity (VSW) and planetary A index (AP, a GMD index) with MS incidence in Tehran and western Greece, during the 23rd solar cycle (1996–2008), by an ecological-correlational study.
Results: We found moderate to strong correlations among MS incidence of Tehran with VSW (rS = 0.665, P = 0.013), with 1 year delay, and also with AP (rS = 0.864, P = 0.001) with 2 year delay. There were very strong correlations among MS incidence data of Greece with VSW (r = 0.906, P < 0.001) and with AP (r = 0.844, P = 0.001), both with 1 year lag.
Conclusion: It is the first time that a hypothesis has introduced an environmental factor that may describe MS incidence alterations; however, it should be reminded that correlation does not mean necessarily the existence of a causal relationship. Important message of these findings for researchers is to provide MS incidence reports with higher resolution for consecutive years, based on the time of disease onset and relapses, not just the time of diagnosis. Then, it would be possible to further investigate the validity of GMD hypothesis or any other probable environmental risk factors.
PMCID: PMC4187332  PMID: 25295148
Multiple Sclerosis; Incidence; Geomagnetic Disturbance; Solar Wind Velocity; Environmental Risk Factor
2.  Anaplasma marginale msp1α Genotypes Evolved under Positive Selection Pressure but Are Not Markers for Geographic Isolates 
Journal of Clinical Microbiology  2003;41(4):1609-1616.
Anaplasma marginale (order Rickettsiales, family Anaplasmataceae), a tick-borne pathogen of cattle, is endemic in tropical and subtropical regions of the world. Many geographic isolates of A. marginale occur in the United States and have been identified by major surface protein 1a (MSP1a), which varies in sequence and molecular weight due to different numbers of tandem 28- to 29-amino-acid repeats. The present study was undertaken to examine the genetic variations among isolates of A. marginale obtained during 2001 from infected cattle from east-central Oklahoma, where A. marginale is endemic. The gene and protein sequences of MSP1a and msp4 nucleotide sequences were used to infer the phylogenetic relationships among Oklahoma and New World isolates from Argentina, Brazil, Mexico, and the United States. All 11 A. marginale isolates collected from Oklahoma had different MSP1a sequences but identical MSP4 sequences. The phylogenies of the msp4 sequences of 13 isolates from Oklahoma in comparison with those of 7 Latin American isolates and 12 U.S. isolates by maximum-parsimony (MP) and maximum-likelihood (ML) analyses, with A. centrale and A. ovis sequences used as outgroups, provided strong bootstrap analysis support for a Latin American clade. Isolates of A. marginale from the southern United States (Florida, Mississippi, and Virginia) and the west-central United States (California, Idaho, Illinois, Oregon, Missouri, and Texas) also grouped into two clades. Both clades contained isolates from Oklahoma, suggesting extensive cattle movement. ML analysis of the msp4 sequences of isolates from Oklahoma provided bootstrap analysis support for east-central and north-central clades in Oklahoma, and both clades included isolates from Stillwater, Okla. Analysis of the codon and amino acid changes among the msp4 sequences of isolates with different phylogenies provided evidence that msp4 is not under positive selection pressure. In contrast, the phylogenies of the MSP1a DNA and protein sequences of 13 isolates from Oklahoma in comparison with those of 7 Latin American and 13 isolates from the United States by MP and ML analyses demonstrated no geographic clustering and provided evidence that this gene is under positive selection pressure. The results indicate that msp1α is not a marker for the characterization of A. marginale geographic isolates and suggest that the genetic heterogeneity observed among isolates of A. marginale within Oklahoma could be explained by cattle movement and the maintenance of different genotypes by independent transmission events.
doi:10.1128/JCM.41.4.1609-1616.2003
PMCID: PMC153873  PMID: 12682152
3.  Characterization of Regional Influenza Seasonality Patterns in China and Implications for Vaccination Strategies: Spatio-Temporal Modeling of Surveillance Data 
PLoS Medicine  2013;10(11):e1001552.
Cécile Viboud and colleagues describe epidemiological patterns of influenza incidence across China to support the design of a national vaccination program.
Please see later in the article for the Editors' Summary
Background
The complexity of influenza seasonal patterns in the inter-tropical zone impedes the establishment of effective routine immunization programs. China is a climatologically and economically diverse country, which has yet to establish a national influenza vaccination program. Here we characterize the diversity of influenza seasonality in China and make recommendations to guide future vaccination programs.
Methods and Findings
We compiled weekly reports of laboratory-confirmed influenza A and B infections from sentinel hospitals in cities representing 30 Chinese provinces, 2005–2011, and data on population demographics, mobility patterns, socio-economic, and climate factors. We applied linear regression models with harmonic terms to estimate influenza seasonal characteristics, including the amplitude of annual and semi-annual periodicities, their ratio, and peak timing. Hierarchical Bayesian modeling and hierarchical clustering were used to identify predictors of influenza seasonal characteristics and define epidemiologically-relevant regions. The annual periodicity of influenza A epidemics increased with latitude (mean amplitude of annual cycle standardized by mean incidence, 140% [95% CI 128%–151%] in the north versus 37% [95% CI 27%–47%] in the south, p<0.0001). Epidemics peaked in January–February in Northern China (latitude ≥33°N) and April–June in southernmost regions (latitude <27°N). Provinces at intermediate latitudes experienced dominant semi-annual influenza A periodicity with peaks in January–February and June–August (periodicity ratio >0.6 in provinces located within 27.4°N–31.3°N, slope of latitudinal gradient with latitude −0.016 [95% CI −0.025 to −0.008], p<0.001). In contrast, influenza B activity predominated in colder months throughout most of China. Climate factors were the strongest predictors of influenza seasonality, including minimum temperature, hours of sunshine, and maximum rainfall. Our main study limitations include a short surveillance period and sparse influenza sampling in some of the southern provinces.
Conclusions
Regional-specific influenza vaccination strategies would be optimal in China; in particular, annual campaigns should be initiated 4–6 months apart in Northern and Southern China. Influenza surveillance should be strengthened in mid-latitude provinces, given the complexity of seasonal patterns in this region. More broadly, our findings are consistent with the role of climatic factors on influenza transmission dynamics.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Every year, millions of people worldwide catch influenza, a viral disease of the airways. Most infected individuals recover quickly but seasonal influenza outbreaks (epidemics) kill about half a million people annually. These epidemics occur because antigenic drift—frequent small changes in the viral proteins to which the immune system responds—means that an immune response produced one year provides only partial protection against influenza the next year. Annual vaccination with a mixture of killed influenza viruses of the major circulating strains boosts this natural immunity and greatly reduces the risk of catching influenza. Consequently, many countries run seasonal influenza vaccination programs. Because the immune response induced by vaccination decays within 4–8 months of vaccination and because of antigenic drift, it is important that these programs are initiated only a few weeks before the onset of local influenza activity. Thus, vaccination starts in early autumn in temperate zones (regions of the world that have a mild climate, part way between a tropical and a polar climate), because seasonal influenza outbreaks occur in the winter months when low humidity and low temperatures favor the transmission of the influenza virus.
Why Was This Study Done?
Unlike temperate regions, seasonal influenza patterns are very diverse in tropical countries, which lie between latitudes 23.5°N and 23.5°S, and in the subtropical countries slightly north and south of these latitudes. In some of these countries, there is year-round influenza activity, in others influenza epidemics occur annually or semi-annually (twice yearly). This complexity, which is perhaps driven by rainfall fluctuations, complicates the establishment of effective routine immunization programs in tropical and subtropical countries. Take China as an example. Before a national influenza vaccination program can be established in this large, climatologically diverse country, public-health experts need a clear picture of influenza seasonality across the country. Here, the researchers use spatio-temporal modeling of influenza surveillance data to characterize the seasonality of influenza A and B (the two types of influenza that usually cause epidemics) in China, to assess the role of putative drivers of seasonality, and to identify broad epidemiological regions (areas with specific patterns of disease) that could be used as a basis to optimize the timing of future Chinese vaccination programs.
What Did the Researchers Do and Find?
The researchers collected together the weekly reports of laboratory-confirmed influenza prepared by the Chinese national sentinel hospital-based surveillance network between 2005 and 2011, data on population size and density, mobility patterns, and socio-economic factors, and daily meteorological data for the cities participating in the surveillance network. They then used various statistical modeling approaches to estimate influenza seasonal characteristics, to assess predictors of influenza seasonal characteristics, and to identify epidemiologically relevant regions. These analyses indicate that, over the study period, northern provinces (latitudes greater than 33°N) experienced winter epidemics of influenza A in January–February, southern provinces (latitudes less than 27°N) experienced peak viral activity in the spring (April–June), and provinces at intermediate latitudes experienced semi-annual epidemic cycles with infection peaks in January–February and June–August. By contrast, influenza B activity predominated in the colder months throughout China. The researchers also report that minimum temperatures, hours of sunshine, and maximum rainfall were the strongest predictors of influenza seasonality.
What Do These Findings Mean?
These findings show that influenza seasonality in China varies between regions and between influenza virus types and suggest that, as in other settings, some of these variations might be associated with specific climatic factors. The accuracy of these findings is limited by the short surveillance period, by sparse surveillance data from some southern and mid-latitude provinces, and by some aspects of the modeling approach used in the study. Further surveillance studies need to be undertaken to confirm influenza seasonality patterns in China. Overall, these findings suggest that, to optimize routine influenza vaccination in China, it will be necessary to stagger the timing of vaccination over three broad geographical regions. More generally, given that there is growing interest in rolling out national influenza immunization programs in low- and middle-income countries, these findings highlight the importance of ensuring that vaccination strategies are optimized by taking into account local disease patterns.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/ 10.1371/journal.pmed.1001552.
This study is further discussed in a PLOS Medicine Perspective by Steven Riley
The UK National Health Service Choices website provides information for patients about seasonal influenza and about influenza vaccination
The World Health Organization provides information on seasonal influenza (in several languages) and on influenza surveillance and monitoring
The US Centers for Disease Control and Prevention also provides information for patients and health professionals on all aspects of seasonal influenza, including information about vaccination; its website contains a short video about personal experiences of influenza.
Flu.gov, a US government website, provides access to information on seasonal influenza and vaccination
Information about the Chinese National Influenza Center, which is part of the Chinese Center for Disease Control and Prevention: and which runs influenza surveillance in China, is available (in English and Chinese)
MedlinePlus has links to further information about influenza and about vaccination (in English and Spanish)
A recent PLOS Pathogens Research Article by James D. Tamerius et al. investigates environmental predictors of seasonal influenza epidemics across temperate and tropical climates
A study published in PLOS ONE by Wyller Alencar de Mello et al. indicates that Brazil, like China, requires staggered timing of vaccination from Northern to Southern states to account for different timings of influenza activity.
doi:10.1371/journal.pmed.1001552
PMCID: PMC3864611  PMID: 24348203
4.  Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates 
Malaria Journal  2007;6:95.
Background
The C-terminal region of merozoite surface protein-1 (MSP-1) is one of the leading candidates for vaccination against the erythrocytic stages of malaria. However, a major concern in the development of MSP-1 based malaria vaccine is the polymorphism observed in different geographical Plasmodium falciparum isolates. To explore whether the sequence heterogeneity of PfMSP-1 leads to variation in naturally acquired anti-MSP-119 antibodies, the present study was undertaken to study PfMSP-119 sequence polymorphism in malaria-endemic villages in eastern India and also carried out a competition enzyme-linked immunosorbent assay using three PfMSP-119 variant forms.
Methods
The sequence variations in the C-terminal region of PfMSP-119 were determined in a malaria endemic region. Three PfMSP-119 variants were produced in Escherichia coli (PfMSP119QKNG-L, PfMSP119EKNG-L and PfMSP119ETSR-F) and an immunodepletion assay was carried out using the corresponding patients' sera.
Results
Results revealed predominance of PfMAD20 allele among Indian field isolates. Seven PfMSP-119 variant forms were isolated in a singe geographical location. Three of PfMSP-119 variant forms when expressed in E. coli showed presence of cross-reaction as well as variant specific antibodies in malaria infected patient sera.
Conclusion
The present study demonstrates the existence of allele specific antibodies in P. falciparum-infected patient sera, however their role in protection requires further investigation. These results thereby, suggest the importance of a multi-allelic PfMSP-119 based vaccine for an effective malaria control.
doi:10.1186/1475-2875-6-95
PMCID: PMC1950510  PMID: 17659072
5.  Oscillating magnetic field disrupts magnetic orientation in Zebra finches, Taeniopygia guttata 
Frontiers in Zoology  2009;6:25.
Background
Zebra finches can be trained to use the geomagnetic field as a directional cue for short distance orientation. The physical mechanisms underlying the primary processes of magnetoreception are, however, largely unknown. Two hypotheses of how birds perceive magnetic information are mainly discussed, one dealing with modulation of radical pair processes in retinal structures, the other assuming that iron deposits in the upper beak of the birds are involved. Oscillating magnetic fields in the MHz range disturb radical pair mechanisms but do not affect magnetic particles. Thus, application of such oscillating fields in behavioral experiments can be used as a diagnostic tool to decide between the two alternatives.
Methods
In a setup that eliminates all directional cues except the geomagnetic field zebra finches were trained to search for food in the magnetic north/south axis. The birds were then tested for orientation performance in two magnetic conditions. In condition 1 the horizontal component of the geomagnetic field was shifted by 90 degrees using a helmholtz coil. In condition 2 a high frequently oscillating field (1.156 MHz) was applied in addition to the shifted field. Another group of birds was trained to solve the orientation task, but with visual landmarks as directional cue. The birds were then tested for their orientation performance in the same magnetic conditions as applied for the first experiment.
Results
The zebra finches could be trained successfully to orient in the geomagnetic field for food search in the north/south axis. They were also well oriented in test condition 1, with the magnetic field shifted horizontally by 90 degrees. In contrast, when the oscillating field was added, the directional choices during food search were randomly distributed. Birds that were trained to visually guided orientation showed no difference of orientation performance in the two magnetic conditions.
Conclusion
The results indicate that zebra finches use a receptor that bases on radical pair processes for sensing the direction of the earth magnetic field in this short distance orientation behavior.
doi:10.1186/1742-9994-6-25
PMCID: PMC2774300  PMID: 19852792
6.  Diversity and population structure of Plasmodium falciparum in Thailand based on the spatial and temporal haplotype patterns of the C-terminal 19-kDa domain of merozoite surface protein-1 
Malaria Journal  2014;13:54.
Background
The 19-kDa C-terminal region of the merozoite surface protein-1 of the human malaria parasite Plasmodium falciparum (PfMSP-119) constitutes the major component on the surface of merozoites and is considered as one of the leading candidates for asexual blood stage vaccines. Because the protein exhibits a level of sequence variation that may compromise the effectiveness of a vaccine, the global sequence diversity of PfMSP-119 has been subjected to extensive research, especially in malaria endemic areas. In Thailand, PfMSP-119 sequences have been derived from a single parasite population in Tak province, located along the Thailand-Myanmar border, since 1995. However, the extent of sequence variation and the spatiotemporal patterns of the MSP-119 haplotypes along the Thai borders with Laos and Cambodia are unknown.
Methods
Sixty-three isolates of P. falciparum from five geographically isolated populations along the Thai borders with Myanmar, Laos and Cambodia in three transmission seasons between 2002 and 2008 were collected and culture-adapted. The msp-1 gene block 17 was sequenced and analysed for the allelic diversity, frequency and distribution patterns of PfMSP-119 haplotypes in individual populations. The PfMSP-119 haplotype patterns were then compared between parasite populations to infer the population structure and genetic differentiation of the malaria parasite.
Results
Five conserved polymorphic positions, which accounted for five distinct haplotypes, of PfMSP-119 were identified. Differences in the prevalence of PfMSP-119 haplotypes were detected in different geographical regions, with the highest levels of genetic diversity being found in the Kanchanaburi and Ranong provinces along the Thailand-Myanmar border and Trat province located at the Thailand-Cambodia border. Despite this variability, the distribution patterns of individual PfMSP-119 haplotypes seemed to be very similar across the country and over the three malarial transmission seasons, suggesting that gene flow may operate between parasite populations circulating in Thailand and the three neighboring countries.
Conclusion
The major MSP-119 haplotypes of P. falciparum populations in all endemic populations during three transmission seasons in Thailand were identified, providing basic information on the common haplotypes of MSP-119 that is of use for malaria vaccine development and inferring the population structure of P. falciparum populations in Thailand.
doi:10.1186/1475-2875-13-54
PMCID: PMC3931489  PMID: 24521474
Allelic polymorphism; DNA sequencing; Merozoite surface antigen; Population structure; Southeast Asia
7.  Testing the Water–Energy Theory on American Palms (Arecaceae) Using Geographically Weighted Regression 
PLoS ONE  2011;6(11):e27027.
Water and energy have emerged as the best contemporary environmental correlates of broad-scale species richness patterns. A corollary hypothesis of water–energy dynamics theory is that the influence of water decreases and the influence of energy increases with absolute latitude. We report the first use of geographically weighted regression for testing this hypothesis on a continuous species richness gradient that is entirely located within the tropics and subtropics. The dataset was divided into northern and southern hemispheric portions to test whether predictor shifts are more pronounced in the less oceanic northern hemisphere. American palms (Arecaceae, n = 547 spp.), whose species richness and distributions are known to respond strongly to water and energy, were used as a model group. The ability of water and energy to explain palm species richness was quantified locally at different spatial scales and regressed on latitude. Clear latitudinal trends in agreement with water–energy dynamics theory were found, but the results did not differ qualitatively between hemispheres. Strong inherent spatial autocorrelation in local modeling results and collinearity of water and energy variables were identified as important methodological challenges. We overcame these problems by using simultaneous autoregressive models and variation partitioning. Our results show that the ability of water and energy to explain species richness changes not only across large climatic gradients spanning tropical to temperate or arctic zones but also within megathermal climates, at least for strictly tropical taxa such as palms. This finding suggests that the predictor shifts are related to gradual latitudinal changes in ambient energy (related to solar flux input) rather than to abrupt transitions at specific latitudes, such as the occurrence of frost.
doi:10.1371/journal.pone.0027027
PMCID: PMC3207816  PMID: 22073244
8.  Avian orientation at steep angles of inclination: experiments with migratory white-crowned sparrows at the magnetic North Pole. 
The Earth's magnetic field and celestial cues provide animals with compass information during migration. Inherited magnetic compass courses are selected based on the angle of inclination, making it difficult to orient in the near vertical fields found at high geomagnetic latitudes. Orientation cage experiments were performed at different sites in high Arctic Canada with adult and young white-crowned sparrows (Zonotrichia leucophrys gambelii) in order to investigate birds' ability to use the Earth's magnetic field and celestial cues for orientation in naturally very steep magnetic fields at and close to the magnetic North Pole. Experiments were performed during the natural period of migration at night in the local geomagnetic field under natural clear skies and under simulated total overcast conditions. The experimental birds failed to select a meaningful magnetic compass course under overcast conditions at the magnetic North Pole, but could do so in geomagnetic fields deviating less than 3 degrees from the vertical. Migratory orientation was successful at all sites when celestial cues were available.
doi:10.1098/rspb.2001.1736
PMCID: PMC1088826  PMID: 11564346
9.  Spatiotemporal Variation in Avian Migration Phenology: Citizen Science Reveals Effects of Climate Change 
PLoS ONE  2012;7(2):e31662.
A growing number of studies have documented shifts in avian migratory phenology in response to climate change, and yet there is a large amount of unexplained variation in the magnitude of those responses across species and geographic regions. We use a database of citizen science bird observations to explore spatiotemporal variation in mean arrival dates across an unprecedented geographic extent for 18 common species in North America over the past decade, relating arrival dates to mean minimum spring temperature. Across all species and geographic locations, species shifted arrival dates 0.8 days earlier for every °C of warming of spring temperature, but it was common for some species in some locations to shift as much as 3–6 days earlier per °C. Species that advanced arrival dates the earliest in response to warming were those that migrate more slowly, short distance migrants, and species with broader climatic niches. These three variables explained 63% of the interspecific variation in phenological response. We also identify a latitudinal gradient in the average strength of phenological response, with species shifting arrival earlier at southern latitudes than northern latitudes for the same degree of warming. This observation is consistent with the idea that species must be more phenologically sensitive in less seasonal environments to maintain the same degree of precision in phenological timing.
doi:10.1371/journal.pone.0031662
PMCID: PMC3285173  PMID: 22384050
10.  Sequence analysis, expression, and binding activity of recombinant major outer sheath protein (Msp) of Treponema denticola. 
Journal of Bacteriology  1996;178(9):2489-2497.
The gene encoding the major outer sheath protein (Msp) of the oral spirochete Treponema denticola ATCC 35405 was cloned, sequenced, and expressed in Escherichia coli. Preliminary sequence analysis showed that the 5' end of the msp gene was not present on the 5.5-kb cloned fragment described in a recent study (M. Haapasalo, K. H. Müller, V. J. Uitto, W. K. Leung, and B. C. McBride, Infect. Immun. 60:2058-2065,1992). The 5' end of msp was obtained by PCR amplification from a T. denticola genomic library, and an open reading frame of 1,629 bp was identified as the coding region for Msp by combining overlapping sequences. The deduced peptide consisted of 543 amino acids and had a molecular mass of 58,233 Da. The peptide had a typical prokaryotic signal sequence with a potential cleavage site for signal peptidase 1. Northern (RNA) blot analysis showing the msp transcript to be approximately 1.7 kb was consistent with the identification of a promoter consensus sequence located optimally upstream of msp and a transcription termination signal found downstream of the stop codon. The entire msp sequence was amplified from T. denticola genomic DNA and cloned in E. coli by using a tightly regulated T7 RNA polymerase vector system. Expression of Msp was toxic to E. coli when the entire msp gene was present. High levels of Msp were produced as inclusion bodies when the putative signal peptide sequence was deleted and replaced by a vector-encoded T7 peptide sequence. Recombinant Msp purified to homogeneity from a clone containing the full-length msp gene adhered to immobilized laminin and fibronectin but not to bovine serum albumin. Attachment of recombinant Msp was decreased in the presence of soluble substrate. Attachment of T. denticola to immobilized laminin and fibronectin was increased by pretreatment of the substrate with recombinant Msp. These studies lend further support to the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola.
PMCID: PMC177970  PMID: 8626313
11.  Low Level of Sequence Diversity at Merozoite Surface Protein-1 Locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai Isolates 
PLoS ONE  2013;8(3):e58962.
Background
The merozoite surface protein-1 (MSP-1) is a candidate target for the development of blood stage vaccines against malaria. Polymorphism in MSP-1 can be useful as a genetic marker for strain differentiation in malarial parasites. Although sequence diversity in the MSP-1 locus has been extensively analyzed in field isolates of Plasmodium falciparum and P. vivax, the extent of variation in its homologues in P. ovale curtisi and P. ovale wallikeri, remains unknown.
Methodology/Principal Findings
Analysis of the mitochondrial cytochrome b sequences of 10 P. ovale isolates from symptomatic malaria patients from diverse endemic areas of Thailand revealed co-existence of P. ovale curtisi (n = 5) and P. ovale wallikeri (n = 5). Direct sequencing of the PCR-amplified products encompassing the entire coding region of MSP-1 of P. ovale curtisi (PocMSP-1) and P. ovale wallikeri (PowMSP-1) has identified 3 imperfect repeated segments in the former and one in the latter. Most amino acid differences between these proteins were located in the interspecies variable domains of malarial MSP-1. Synonymous nucleotide diversity (πS) exceeded nonsynonymous nucleotide diversity (πN) for both PocMSP-1 and PowMSP-1, albeit at a non-significant level. However, when MSP-1 of both these species was considered together, πS was significantly greater than πN (p<0.0001), suggesting that purifying selection has shaped diversity at this locus prior to speciation. Phylogenetic analysis based on conserved domains has placed PocMSP-1 and PowMSP-1 in a distinct bifurcating branch that probably diverged from each other around 4.5 million years ago.
Conclusion/Significance
The MSP-1 sequences support that P. ovale curtisi and P. ovale wallikeri are distinct species. Both species are sympatric in Thailand. The low level of sequence diversity in PocMSP-1 and PowMSP-1 among Thai isolates could stem from persistent low prevalence of these species, limiting the chance of outcrossing at this locus.
doi:10.1371/journal.pone.0058962
PMCID: PMC3594193  PMID: 23536840
12.  Temporal Variation in Population Size of European Bird Species: Effects of Latitude and Marginality of Distribution  
PLoS ONE  2013;8(10):e77654.
In the Northern Hemisphere, global warming has been shown to affect animal populations in different ways, with southern populations in general suffering more from increased temperatures than northern populations of the same species. However, southern populations are also often marginal populations relative to the entire breeding range, and marginality may also have negative effects on populations. To disentangle the effects of latitude (possibly due to global warming) and marginality on temporal variation in population size, we investigated European breeding bird species across a latitudinal gradient. Population size estimates were regressed on years, and from these regressions we obtained the slope (a proxy for population trend) and the standard error of the estimate (SEE) (a proxy for population fluctuations). The possible relationships between marginality or latitude on one hand and slopes or SEE on the other were tested among populations within species. Potentially confounding factors such as census method, sampling effort, density-dependence, habitat fragmentation and number of sampling years were controlled statistically. Population latitude was positively related to regression slopes independent of marginality, with more positive slopes (i.e., trends) in northern than in southern populations. The degree of marginality was positively related to SEE independent of latitude, with marginal populations showing larger SEE (i.e., fluctuations) than central ones. Regression slopes were also significantly related to our estimate of density-dependence and SEE was significantly affected by the census method. These results are consistent with a scenario in which southern and northern populations of European bird species are negatively affected by marginality, with southern populations benefitting less from global warming than northern populations, thus potentially making southern populations more vulnerable to extinction.
doi:10.1371/journal.pone.0077654
PMCID: PMC3798344  PMID: 24147048
13.  Altered Orientation and Flight Paths of Pigeons Reared on Gravity Anomalies: A GPS Tracking Study 
PLoS ONE  2013;8(10):e77102.
The mechanisms of pigeon homing are still not understood, in particular how they determine their position at unfamiliar locations. The “gravity vector” theory holds that pigeons memorize the gravity vector at their home loft and deduct home direction and distance from the angular difference between memorized and actual gravity vector. However, the gravity vector is tilted by different densities in the earth crust leading to gravity anomalies. We predicted that pigeons reared on different gravity anomalies would show different initial orientation and also show changes in their flight path when crossing a gravity anomaly. We reared one group of pigeons in a strong gravity anomaly with a north-to-south gravity gradient, and the other group of pigeons in a normal area but on a spot with a strong local anomaly with a west-to-east gravity gradient. After training over shorter distances, pigeons were released from a gravitationally and geomagnetically normal site 50 km north in the same direction for both home lofts. As expected by the theory, the two groups of pigeons showed divergent initial orientation. In addition, some of the GPS-tracked pigeons also showed changes in their flight paths when crossing gravity anomalies. We conclude that even small local gravity anomalies at the birth place of pigeons may have the potential to bias the map sense of pigeons, while reactivity to gravity gradients during flight was variable and appeared to depend on individual navigational strategies and frequency of position updates.
doi:10.1371/journal.pone.0077102
PMCID: PMC3806762  PMID: 24194860
14.  North Atlantic Oscillation and timing of spring migration in birds. 
Migrant birds have been trapped on the island of Helgoland (southeastern North Sea) since 1909, with methods and sampling effort remaining unchanged throughout the last four decades. In 12 short/medium-distance migrants and 12 long-distance migrants (23 passerines plus the European woodcock) sample sizes were sufficient to calculate mean spring passage (msp) times and to relate these to climate change. All but one species, passing Helgoland en route to their breeding areas (mainly in Scandinavia), show a trend towards earlier msp-time, which is significant in 7 short/medium-distance migrants and 10 long-distance migrants. The msp-times advanced by 0.05-0.28 days per year, short/medium-distance migrants not differing from long-distance migrants. In 23 out of the 24 species, earlier msp-times coincide with local warmer msp-temperatures (significantly in 11 and 7 species of the two groups, respectively). Even more striking is the relation to a large-scale phenomenon, the North Atlantic Oscillation (NAO), during the last four decades. Again, in 23 out of the 24 species, an earlier msp-time coincides with higher NAO indices (significantly in 9 and 12 species, respectively). The NAO index can also explain differences and similarities in spring migration strategies, as well as migration routes within Europe.
doi:10.1098/rspb.2002.2236
PMCID: PMC1691241  PMID: 12614571
15.  Phase 1 Study of Two Merozoite Surface Protein 1 (MSP142) Vaccines for Plasmodium falciparum Malaria 
PLoS Clinical Trials  2007;2(4):e12.
Objectives:
To assess the safety and immunogenicity of two vaccines, MSP142-FVO/Alhydrogel and MSP142-3D7/Alhydrogel, targeting blood-stage Plasmodium falciparum parasites.
Design:
A Phase 1 open-label, dose-escalating study.
Setting:
Quintiles Phase 1 Services, Lenexa, Kansas between July 2004 and November 2005.
Participants:
Sixty healthy malaria-naïve volunteers 18–48 y of age.
Interventions:
The C-terminal 42-kDa region of merozoite surface protein 1 (MSP142) corresponding to the two allelic forms present in FVO and 3D7 P. falciparum lines were expressed in Escherichia coli, refolded, purified, and formulated on Alhydrogel (aluminum hydroxide). For each vaccine, volunteers in each of three dose cohorts (5, 20, and 80 μg) were vaccinated at 0, 28, and 180 d. Volunteers were followed for 1 y.
Outcome Measures:
The safety of MSP142-FVO/Alhydrogel and MSP142-3D7/Alhydrogel was assessed. The antibody response to each vaccine was measured by reactivity to homologous and heterologous MSP142, MSP119, and MSP133 recombinant proteins and recognition of FVO and 3D7 parasites.
Results:
Anti-MSP142 antibodies were detected by ELISA in 20/27 (74%) and 22/27 (81%) volunteers receiving three vaccinations of MSP142-FVO/Alhydrogel or MSP142-3D7/Alhydrogel, respectively. Regardless of the vaccine, the antibodies were cross-reactive to both MSP142-FVO and MSP142-3D7 proteins. The majority of the antibody response targeted the C-terminal 19-kDa domain of MSP142, although low-level antibodies to the N-terminal 33-kDa domain of MSP142 were also detected. Immunofluorescence microscopy of sera from the volunteers demonstrated reactivity with both FVO and 3D7 P. falciparum schizonts and free merozoites. Minimal in vitro growth inhibition of FVO or 3D7 parasites by purified IgG from the sera of the vaccinees was observed.
Conclusions:
The MSP142/Alhydrogel vaccines were safe and well tolerated but not sufficiently immunogenic to generate a biologic effect in vitro. Addition of immunostimulants to the Alhydrogel formulation to elicit higher vaccine-induced responses in humans may be required for an effective vaccine.
Editorial Commentary
Background: Generally, adults living in parts of the world where malaria is common develop protective immunity against the parasite. This means they may get infected but not become ill as a result. However, there are individuals, such as pregnant women and children under the age of five, who are more likely to develop symptoms of malaria due to no (or reduced) natural immunity. A successful malaria vaccine would stimulate an individual's immune system to respond to the malaria parasite and prevent serious clinical disease. Many different groups are currently developing potential vaccines. Several candidates are based on a protein called MSP1 (merozoite surface protein 1) which is found on the surface of the blood-stage form of the malaria parasite. However, in nature parasites carry different versions of the MSP1 protein, and ideally a successful vaccine would bring about immune responses against these different versions. The researchers carrying out this trial wanted to compare the safety and immune responses against candidate vaccines representing two different MSP1 proteins, which covered many different parasite lines. As a phase 1 trial, the study was carried out in healthy adult volunteers. Sixty individuals were assigned to receive an injection of the vaccines, either containing a recombinant protein analogous to the FVO parasite line (termed MSP142-FVO) or the 3D7 parasite line (termed MSP142-3D7) at three different dose levels. The trial's primary objective was to assess safety, which was done by collecting data on any abnormal signs or symptoms up to 14 d after each of three vaccinations. These outcomes were graded and then defined as related to the vaccine or not. The researchers also looked at antibody levels in participants' blood against different variants of the MSP1 protein, as well as using in vitro tests to see whether antibodies from vaccinated individuals could prevent malaria parasites from growing in lab culture.
What the trial shows: The safety outcomes of the trial showed that the most common type of side effect experienced by the volunteers was pain at the injection site. The vast majority of such events were graded as mild, although there was one single case of a severe event (high levels of pain experienced by one volunteer at the injection site). There was no significant association between the chance of side effects and the vaccine dosage that an individual received. Following vaccination, antibody levels against the protein on which the vaccine was based were detected, although these levels dropped over time. The researchers did not see a strong association between the vaccine dosage that individuals received and the level of antibody response. However, the two vaccines when compared seemed to be equally good at raising an immune response and both caused antibodies to be raised corresponding to different variants of the MSP1 protein. However, the antibodies raised did not seem to be particularly effective at preventing malaria parasites from growing in lab culture.
Strengths and limitations: Strengths of this study include a comparison of three different dosage levels of the vaccines under study, as well as a comparison of two vaccines based on the same protein, representing different parasite lines. Limitations to the study include the small number of participants, which makes the trial underpowered to detect all but large differences in side effects between the groups being compared. A placebo arm was not included in the trial, so it is not possible to be sure that the numbers of side effects observed here can be attributed to the vaccines or not. Finally, the procedure for assigning individuals to the two different vaccines involved alternation, rather than true randomization, which could have minimized the risk of bias.
Contribution to the evidence: The trial reported here is an essential step in vaccine development. The results provide the first evidence relating to safety for these two vaccines, and do not raise any safety concerns at this stage. Although the vaccines raised an immune response, the antibodies raised did not seem to have much of an effect on malaria parasites in vitro. While these vaccines are safe, alternative MSP1 vaccine formulations anticipated to bring about a greater immune response will likely be studied before proceeding to field studies.
doi:10.1371/journal.pctr.0020012
PMCID: PMC1847697  PMID: 17415408
16.  Analysis of genetic polymorphism in select vaccine candidate antigens and microsatellite loci in Plasmodium falciparum from endemic areas at varying altitudes 
Acta tropica  2007;102(3):201-205.
Plasmodium falciparum parasites obtained from symptomatic patients attending clinics in Bindura (altitude 1,100 m), Chiredzi (600 m) and Kariba (< 600 m), previously reported to differ in malaria endemicity were genotyped on the msp-1, msp-2 and glurp loci to examine the extent of parasite genetic diversity. While the parasites were monomorphic for msp-1 allele RO33 from the three locations, the K1 allele was overrepresented in Kariba (p=0.02) and Mad20 alleles occurred at a higher frequency in Bindura. A similar PCR analysis for glurp and the two main allelic families of msp-2, i.e IC/3D7 and FC-27 revealed minimal differences in the parasite population. A total of 8 msp-1 Block 2 and 11 msp-2 genotypes were identified from the three locations combined. On the glurp locus, thirteen different genotypes ranging in size from 660 to 1160 bp were detected in parasites obtained from Bindura and Kariba. To gain further insight into P. falciparum genetic diversity in the three different geographical locations, parasites were examined for neutral microsatellite markers (C4M8, C13M30 and TA81). The number of microsatellite alleles ranged from 8 to 17 and the average expected heterozygosity (HE) for the three areas combined was 0.83 suggesting that the parasite population of Zimbabwe is genetically heterogeneous. These findings have implications in understanding the impact of genetic variation on immunity and possibly emergence of drug resistance.
doi:10.1016/j.actatropica.2007.05.001
PMCID: PMC2692884  PMID: 17568548
17.  Characterization of Bacterial Magnetotactic Behaviors by Using a Magnetospectrophotometry Assay▿  
Applied and Environmental Microbiology  2009;75(12):3835-3841.
Magnetotactic bacteria have the unique capacity of synthesizing intracellular single-domain magnetic particles called magnetosomes. The magnetosomes are usually organized in a chain that allows the bacteria to align and swim along geomagnetic field lines, a behavior called magnetotaxis. Two mechanisms of magnetotaxis have been described. Axial magnetotactic cells swim in both directions along magnetic field lines. In contrast, polar magnetotactic cells swim either parallel to the geomagnetic field lines toward the North Pole (north seeking) or antiparallel toward the South Pole (south seeking). In this study, we used a magnetospectrophotometry (MSP) assay to characterize both the axial magnetotaxis of “Magnetospirillum magneticum” strain AMB-1 and the polar magnetotaxis of magneto-ovoid strain MO-1. Two pairs of Helmholtz coils were mounted onto the cuvette holder of a common laboratory spectrophotometer to generate two mutually perpendicular homogeneous magnetic fields parallel or perpendicular to the light beam. The application of magnetic fields allowed measurements of the change in light scattering resulting from cell alignment in a magnetic field or in absorbance due to bacteria swimming across the light beam. Our results showed that MSP is a powerful tool for the determination of bacterial magnetism and the analysis of alignment and swimming of magnetotactic bacteria in magnetic fields. Moreover, this assay allowed us to characterize south-seeking derivatives and non-magnetosome-bearing strains obtained from north-seeking MO-1 cultures. Our results suggest that oxygen is a determinant factor that controls magnetotactic behavior.
doi:10.1128/AEM.00165-09
PMCID: PMC2698362  PMID: 19376916
18.  Genetic structure of Plasmodium falciparum field isolates in eastern and north-eastern India 
Malaria Journal  2007;6:60.
Background
Molecular techniques have facilitated the studies on genetic diversity of Plasmodium species particularly from field isolates collected directly from patients. The msp-1 and msp-2 are highly polymorphic markers and the large allelic polymorphism has been reported in the block 2 of the msp-1 gene and the central repetitive domain (block3) of the msp-2 gene. Families differing in nucleotide sequences and in number of repetitive sequences (length variation) were used for genotyping purposes. As limited reports are available on the genetic diversity existing among Plasmodium falciparum population of India, this report evaluates the extent of genetic diversity in the field isolates of P. falciparum in eastern and north-eastern regions of India.
Methods
A study was designed to assess the diversity of msp-1 and msp-2 among the field isolates from India using allele specific nested PCR assays and sequence analysis. Field isolates were collected from five sites distributed in three states namely, Assam, West Bengal and Orissa.
Results
P. falciparum isolates of the study sites are highly diverse in respect of length as well as sequence motifs with prevalence of all the reported allelic families of msp-1 and msp-2. Prevalence of identical allelic composition as well as high level of sequence identity of alleles suggest a considerable amount of gene flow between the P. falciparum populations of different states. A comparatively higher proportion of multiclonal isolates as well as multiplicity of infection (MOI) was observed among isolates of highly malarious districts Karbi Anglong (Assam) and Sundergarh (Orissa). In all the five sites, R033 family of msp-1 was observed to be monomorphic with an allele size of 150/160 bp. The observed 80–90% sequence identity of Indian isolates with data of other regions suggests that Indian P. falciparum population is a mixture of different strains.
Conclusion
The present study shows that the field isolates of eastern and north-eastern regions of India are highly diverse in respect of msp-1 (block 2) and msp-2 (central repeat region, block 3). As expected Indian isolates present a picture of diversity closer to southeast Asia, Papua New Guinea and Latin American countries, regions with low to meso-endemicity of malaria in comparison to African regions of hyper- to holo-endemicity.
doi:10.1186/1475-2875-6-60
PMCID: PMC1892028  PMID: 17517129
19.  The Plasmodium falciparum merozoite surface protein-1 19 KD antibody response in the Peruvian Amazon predominantly targets the non-allele specific, shared sites of this antigen 
Malaria Journal  2010;9:3.
Background
Plasmodium falciparum re-emerged in Iquitos, Peru in 1994 and is now hypoendemic (< 0.5 infections/person/year). Purportedly non-immune individuals with discrete (non-overlapping) P. falciparum infections can be followed using this population dynamic. Previous work demonstrated a strong association between this population's antibody response to PfMSP1-19KD and protection against febrile illness and parasitaemia. Therefore, some selection for PfMSP1-19KD allelic diversity would be expected if the protection is to allele-specific sites of PfMSP1-19KD. Here, the potential for allele-specific polymorphisms in this population is investigated, and the allele-specificity of antibody responses to PfMSP1-19KD are determined.
Methods
The 42KD region in PfMSP1 was genotyped from 160 individual infections collected between 2003 and 2007. Additionally, the polymorphic block 2 region of Pfmsp1 (Pfmsp1-B2) was genotyped in 781 infection-months to provide a baseline for population-level diversity. To test whether PfMSP1-19KD genetic diversity had any impact on antibody responses, ELISAs testing IgG antibody response were performed on individuals using all four allele-types of PfMSP1-19KD. An antibody depletion ELISA was used to test the ability of antibodies to cross-react between allele-types.
Results
Despite increased diversity in Pfmsp1-B2, limited diversity within Pfmsp1-42KD was observed. All 160 infections genotyped were Mad20-like at the Pfmsp1-33KD locus. In the Pfmsp1-19KD locus, 159 (99.4%) were the Q-KSNG-F haplotype and 1 (0.6%) was the E-KSNG-L haplotype. Antibody responses in 105 individuals showed that Q-KNG and Q-TSR alleles generated the strongest immune responses, while Q-KNG and E-KNG responses were more concordant with each other than with those from Q-TSR and E-TSR, and vice versa. The immuno-depletion ELISAs showed all samples responded to the antigenic sites shared amongst all allelic forms of PfMSP1-19KD.
Conclusions
A non-allele specific antibody response in PfMSP1-19KD may explain why other allelic forms have not been maintained or evolved in this population. This has important implications for the use of PfMSP1-19KD as a vaccine candidate. It is possible that Peruvians have increased antibody responses to the shared sites of PfMSP1-19KD, either due to exposure/parasite characteristics or due to a human-genetic predisposition. Alternatively, these allelic polymorphisms are not immune-specific even in other geographic regions, implying these polymorphisms may be less important in immune evasion that previous studies suggest.
doi:10.1186/1475-2875-9-3
PMCID: PMC2818648  PMID: 20047674
20.  Dynamics of Polymorphism in a Malaria Vaccine Antigen at a Vaccine-Testing Site in Mali 
PLoS Medicine  2007;4(3):e93.
Background
Malaria vaccines based on the 19-kDa region of merozoite surface protein 1 (MSP-119) derived from the 3D7 strain of Plasmodium falciparum are being tested in clinical trials in Africa. Knowledge of the distribution and natural dynamics of vaccine antigen polymorphisms in populations in which malaria vaccines will be tested will guide vaccine design and permit distinction between natural fluctuations in genetic diversity and vaccine-induced selection.
Methods and Findings
Using pyrosequencing, six single-nucleotide polymorphisms in the nucleotide sequence encoding MSP-119 were genotyped from 1,363 malaria infections experienced by 100 children who participated in a prospective cohort study in Mali from 1999 to 2001. The frequencies of 14 MSP-119 haplotypes were compared over the course of the malaria transmission season for all three years, in three age groups, and in consecutive infections within individuals. While the frequency of individual MSP-119 haplotypes fluctuated, haplotypes corresponding to FVO and FUP strains of P. falciparum (MSP-119 haplotypes QKSNGL and EKSNGL, respectively) were most prevalent during three consecutive years and in all age groups with overall prevalences of 46% (95% confidence interval [CI] 44%–49%) and 36% (95% CI 34%–39%), respectively. The 3D7 haplotype had a lower overall prevalence of 16% (95% CI 14%–18%). Multiplicity of infection based on MSP-119 was higher at the beginning of the transmission season and in the oldest individuals (aged ≥11 y). Three MSP-119 haplotypes had a reduced frequency in symptomatic infections compared to asymptomatic infections. Analyses of the dynamics of MSP-119 polymorphisms in consecutive infections implicate three polymorphisms (at positions 1691, 1700, and 1701) as being particularly important in determining allele specificity of anti-MSP-119 immunity.
Conclusions
Parasites with MSP-119 haplotypes different from that of the leading vaccine strain were consistently the most prevalent at a vaccine trial site. If immunity elicited by an MSP-1-based vaccine is allele-specific, a vaccine based on either the FVO or FUP strain might have better initial efficacy at this site. This study, to our knowledge the largest of its kind to date, provides molecular information needed to interpret population responses to MSP-1-based vaccines and suggests that certain MSP-119 polymorphisms may be relevant to cross-protective immunity.
Christopher Plowe and colleagues surveyed local malaria parasites for genetic diversity in MSP-1, a candidate vaccine antigen. These data are needed to interpret population responses to MSP-1-based vaccines during trials planned at this site.
Editors' Summary
Background.
Malaria, a tropical parasitic disease, kills about one million people—mainly children—every year. Most of these deaths are caused by Plasmodium falciparum, which is transmitted to humans through the bites of infected mosquitoes. These insects inject a form of the parasite known as sporozoites into people that replicates inside liver cells without causing symptoms. Four to five days later, merozoites (another form of the parasite) are released from the liver cells and invade red blood cells. Here, they replicate 10-fold before bursting out and infecting other red blood cells. This massive increase in parasite burden causes malaria's flu-like symptoms. If untreated, it also causes anemia (a red blood cell deficit) and damages the brain and other organs where parasitized red blood cells sequester. Malaria can be treated with antimalarial drugs and partly prevented by reducing the chances of being bitten by an infected mosquito. In addition, researchers are developing vaccines designed to reduce the global burden of malaria. These contain individual malaria antigens (proteins from the parasite that stimulate an immune response) that should, when injected into people, prime the immune system so that it can rapidly control malaria infections.
Why Was This Study Done?
The development of an effective malaria vaccine is not easy, in part because people can be simultaneously infected with several parasite strains. These often carry different variants (alleles) of the genes encoding antigens, which means that the actual parasite proteins might differ from the ones used for vaccination. If this is the case, the immune response generated by the vaccine might be less effective or even ineffective. An ideal vaccine would therefore stimulate an immune response that recognizes all these strain-specific antigens. However, little is known about their distribution in parasite populations in malarial regions, or about how this distribution changes over time (its dynamics). This information is needed to aid vaccine design and development. In this study, the researchers have investigated the distribution and dynamics of genetic variants of a merozoite antigen called MSP-119, which is included in a vaccine currently being tested in Mali, West Africa. Although most of the MSP-119 sequence is conserved, it contains six strain-specific polymorphisms (genetic variations); the candidate vaccine contains MSP-119 from the 3D7 strain of P. falciparum.
What Did the Researchers Do and Find?
The researchers used rapid DNA sequencing (pyrosequencing) to examine the MSP-119 sequence in more than 1,300 malaria infections in 100 Malian children. They compared the frequencies of 14 MSP-119 haplotypes (sets of polymorphisms at the six variant sites) over three years, in three age groups, and in consecutive infections within individuals. They found that the frequency of individual MSP-119 haplotypes fluctuated in their study population but that those found in P. falciparum FVO and FUP strains were always the commonest, each being present in about 40% of the infections. By contrast, the P. falciparum 3D7 MSP-119 haplotype was present in only 16% of the infections. They also found that mixed infections were more common at the start of each malaria season and in older individuals. In addition, individuals who were infected repeatedly by parasites from different strains (with different MSP-119 variants) seemed to get sick with malaria more often than those infected multiple times by the same strain. The differences might, therefore, be important in determining the specificity of the immune response to MSP-119.
What Do These Findings Mean?
These findings indicate that most parasites that cause malaria at the Malian test site for the malaria vaccine that contains 3D7-specific MSP-119 have a different form of MSP-119. Although early results from field trials suggest that the 3D7-derived vaccine provides some protection against the more common FVO and FUP strains, the immunity stimulated by the vaccine might be mainly allele specific. If this turns out to be the case, these results suggest that a FVO- or FUP-derived vaccine might be more effective in Mali than the 3D7-derived vaccine, though not necessarily elsewhere. More generally, these results show the importance of determining the genetics of pathogen populations before starting vaccine trials. Without this information, a vaccine's ability to prevent infections with specific parasite strains cannot be determined accurately and potentially useful vaccines might be abandoned if they are tested in inappropriate populations. Importantly, baseline information of this sort will also allow vaccine developers to detect any vaccine-induced changes in the pathogen population that might affect the long-term efficacy of their vaccines.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040093.
A related PLoS Medicine Perspective by Colin Sutherland discusses variation in malaria antigens as a challenge in vaccine development
The malaria program of the University of Maryland Center for Vaccine Development performs research on many aspects of malaria
Information on malaria and the development of vaccines is available from the Malaria Vaccine Initiative
The World Health Organization provides links to general information on malaria plus some specific information on malaria vaccine development
MedlinePlus encyclopedia has entries on malaria and on vaccination
US Centers for Disease Control and Prevention provides information for patients and professionals on malaria
US National Institute of Allergy and Infectious Diseases has information on malaria, including research into vaccines
doi:10.1371/journal.pmed.0040093
PMCID: PMC1820605  PMID: 17355170
21.  Identification and characterization of the merozoite surface protein 1 (msp1) gene in a host-generalist avian malaria parasite, Plasmodium relictum (lineages SGS1 and GRW4) with the use of blood transcriptome 
Malaria Journal  2013;12:381.
Background
The merozoite surface protein 1 (msp1) is one of the most studied vaccine candidate genes in mammalian Plasmodium spp. to have been used for investigations of epidemiology, population structures, and immunity to infections. However methodological difficulties have impeded the use of nuclear markers such as msp1 in Plasmodium parasites causing avian malaria. Data from an infection transcriptome of the host generalist avian malaria parasite Plasmodium relictum was used to identify and characterize the msp1 gene from two different isolates (mtDNA lineages SGS1 and GRW4). The aim was to investigate whether the msp1 gene in avian malaria species shares the properties of the msp1 gene in Plasmodium falciparum in terms of block variability, conserved anchor points and repeat motifs, and further to investigate the degree to which the gene might be informative in avian malaria parasites for population and epidemiological studies.
Methods
Reads from 454 sequencing of birds infected with avian malaria was used to develop Sanger sequencing protocols for the msp1 gene of P. relictum. Genetic variability between variable and conserved blocks of the gene was compared within and between avian malaria parasite species, including P. falciparum. Genetic variability of the msp1 gene in P. relictum was compared with six other nuclear genes and the mtDNA gene cytochrome b.
Results
The msp1 gene of P. relictum shares the same general pattern of variable and conserved blocks as found in P. falciparum, although the variable blocks exhibited less variability than P. falciparum. The variation across the gene blocks in P. falciparum spanned from being as conserved as within species variation in P. relictum to being as variable as between the two avian malaria species (P. relictum and Plasmodium gallinaceum) in the variable blocks. In P. relictum the highly conserved p19 region of the peptide was identified, which included two epidermal growth factor-like domains and a fully conserved GPI anchor point.
Conclusion
This study provides protocols for evaluation of the msp1 gene in the avian malaria generalist parasite P. relictum. The msp1 gene in avian Plasmodium shares the genetic properties seen in P. falciparum, indicating evolutionary conserved functions for the gene. The data on the variable blocks of the gene show that the msp1 gene in P. relictum might serve as a good candidate gene for future population and epidemiological studies of the parasite.
doi:10.1186/1475-2875-12-381
PMCID: PMC3827925  PMID: 24172200
Avian malaria; Merozoite surface protein 1; Genetic variation; Plasmodium relictum; SGS1; GRW4
22.  CD4+ T Lymphocytes from Anaplasma marginale Major Surface Protein 2 (MSP2) Vaccinees Recognize Naturally Processed Epitopes Conserved in MSP3  
Infection and Immunity  2004;72(6):3688-3692.
Major surface protein 2 (MSP2) and MSP3 of the persistent bovine ehrlichial pathogen Anaplasma marginale are immunodominant proteins that undergo antigenic variation. The recently completed sequence of MSP3 revealed blocks of amino acids in the N and C termini that are conserved with MSP2. This study tested the hypothesis that CD4+ T cells specific for MSP2 recognize naturally processed epitopes conserved in MSP3. At least one epitope in the N terminus and two in the C terminus of MSP2 were also processed from MSP3 and presented to CD4+ T lymphocytes from MSP2-immunized cattle. This T-lymphocyte response to conserved and partially conserved epitopes may contribute to the immunodominance of MSP2 and MSP3.
doi:10.1128/IAI.72.6.3688-3692.2004
PMCID: PMC415717  PMID: 15155686
23.  Polymorphisms at the Microseminoprotein-beta (MSMB) Locus Associated With Physiological Variation in Beta-Microseminoprotein (β-MSP) and Prostate Specific Antigen (PSA) Levels 
Background
rs10993994, a single nucleotide polymorphism (SNP) at the genetic locus encoding ß-microseminoprotein (β-MSP), is associated with both prostate cancer risk and levels of blood prostate-specific antigen (PSA), a biomarker used in prostate cancer screening. Therefore, we wished to determine the association between SNPs at MSMB, the gene encoding β-MSP, and levels of the prostate-produced biomarkers β-MSP, PSA, and human kallikrein 2 (hK2) in blood and semen.
Methods
Blood and semen from 304 healthy young Swedish men (aged 18-21) were assayed for β-MSP, PSA and hK2. SNPs around MSMB were genotyped from matched DNA and analyzed for quantitative association with biomarker levels. Empirical p-values were multiple test corrected and independence of each SNP’s effect was determined.
Results
rs10993994 is significantly associated with blood and semen levels of β-MSP (both p<1.0×10−7) and PSA (p=0.00014 and p=0.0019), and semen levels of hK2 (p=0.00027). Additional copies of the prostate cancer risk allele resulted in lower β-MSP but higher PSA levels, and singly explained 23% and 5% of the variation seen in semen β-MSP and PSA. Additional SNPs at MSMB are associated with β-MSP and PSA independently of rs10993994.
Conclusions
SNPs at MSMB correlate with physiological variation in β-MSP and PSA levels in the blood and semen of healthy young Swedish men. In particular, rs10993994 has a strong effect on β-MSP levels.
Impact
Our results suggest a mechanism by which rs10993994 may predispose to prostate cancer and raise the possibility that genetic variation may need to be considered in interpreting levels of these biomarkers.
doi:10.1158/1055-9965.EPI-10-0431
PMCID: PMC2946372  PMID: 20696662
PSA; beta-MSP; prostate biomarker; rs10993994; microseminoprotein beta; PSP94; hK2
24.  Characterization of a protective Escherichia coli-expressed Plasmodium falciparum merozoite surface protein 3 indicates a non-linear, multi-domain structure 
Immunization with a recombinant yeast-expressed Plasmodium falciparum merozoite surface protein 3 (MSP3) protected Aotus nancymai monkeys against a virulent challenge infection. Unfortunately, the production process for this yeast-expressed material was not optimal for human trials. In an effort to produce a recombinant MSP3 protein in a scaleable manner, we expressed and purified near-full-length MSP3 in Escherichia coli (EcMSP3). Purified EcMSP3 formed non-globular dimers as determined by analytical size-exclusion HPLC with in-line multi-angle light scatter and quasi-elastic light scatter detection and velocity sedimentation (Rh 7.6 ± 0.2 nm and 6.9 nm, respectively). Evaluation by high-resolution atomic force microscopy revealed non-linear asymmetric structures, with beaded domains and flexible loops that were recognized predominantly as dimers, although monomers and larger multimers were observed. The beaded substructure corresponds to predicted structural domains, which explains the velocity sedimentation results and improves the conceptual model of the protein. Vaccination with EcMSP3 in Freund's adjuvant-induced antibodies that recognized native MSP3 in parasitized erythrocytes by an immunofluorescence assay and gave delayed time to treatment in a group of Aotus monkeys in a virulent challenge infection with the FVO strain of P. falciparum. Three of the seven monkeys vaccinated with EcMSP3 had low peak parasitemias. EcMSP3, which likely mimics the native MSP3 structure located on the merozoite surface, is a viable candidate for inclusion in a multi-component malaria vaccine.
doi:10.1016/j.molbiopara.2008.11.006
PMCID: PMC3633458  PMID: 19073223
Malaria; Plasmodium falciparum; MSP3; Vaccine; Aotus; Escherichia coli
25.  Cohort study of the association of antibody levels to AMA1, MSP119, MSP3 and GLURP with protection from clinical malaria in Ghanaian children 
Malaria Journal  2008;7:142.
Background
Antigen-specific antibody-mediated immune responses play an important role in natural protection against clinical malaria, but conflicting estimates of this association have emerged from immuno-epidemiological studies in different geographical settings. This study was aimed at assessing in a standardized manner the relationship between the antibody responses to four malaria vaccine candidate antigens and protection from clinical malaria, in a cohort of Ghanaian children.
Methods
Standardized ELISA protocols were used to measure isotype and IgG subclass levels to Apical Membrane Antigen 1 (AMA1), Merozoite Surface Protein 1–19 (MSP119), Merozoite Surface Protein 3 (MSP3) and Glutamate Rich Protein (GLURP) antigens in plasma samples from 352 Ghanaian children, aged three to 10 years with subsequent malaria surveillance for nine months. This is one of a series of studies in different epidemiological settings using the same standardized ELISA protocols to permit comparisons of results from different laboratories.
Results
The incidence rate of malaria was 0.35 episodes per child per year. Isotype and IgG subclasses for all antigens investigated increased with age, while the risk of malaria decreased with age. After adjusting for age, higher levels of IgG to GLURP, MSP119, MSP3 and IgM to MSP119, MSP3 and AMA1 were associated with decreased malaria incidence. Of the IgG subclasses, only IgG1 to MSP119 was associated with reduced incidence of clinical malaria. A previous study in the same location failed to find an association of antibodies to MSP119 with clinical malaria. The disagreement may be due to differences in reagents, ELISA and analytical procedures used in the two studies. When IgG, IgM and IgG subclass levels for all four antigens were included in a combined model, only IgG1 [(0.80 (0.67–0.97), p = 0.018)] and IgM [(0.48 (0.32–0.72), p < 0.001)] to MSP119 were independently associated with protection from malaria.
Conclusion
Using standardized procedures, the study has confirmed the importance of antibodies to MSP119 in reducing the risk of clinical malaria in Ghanaian children, thus substantiating its potential as a malaria vaccine candidate.
doi:10.1186/1475-2875-7-142
PMCID: PMC2529305  PMID: 18664257

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