Avian host composition,local speciation and dispersal drive the regional assembly of avian malaria parasites in South American birds

Identifying the ecological factors that shape parasite distributions remains a central goal in disease ecology. These factors include dispersal capability, environmental filters and geographic distance. Using 520 haemosporidian parasite genetic lineages recovered from 7,534 birds sampled across tropical and temperate South America, we tested (a) the latitudinal diversity gradient hypothesis and (b) the distance–decay relationship (decreasing proportion of shared species between communities with increasing geographic distance) for this host–parasite system. We then inferred the biogeographic processes influencing the diversity and distributions of this cosmopolitan group of parasites across South America. We found support for a latitudinal gradient in diversity for avian haemosporidian parasites, potentially mediated through higher avian host diversity towards the equator. Parasite similarity was correlated with climate similarity, geographic distance and host composition. Local diversification in Amazonian lineages followed by dispersal was the most frequent biogeographic events reconstructed for haemosporidian parasites. Combining macroecological patterns and biogeographic processes, our study reveals that haemosporidian parasites are capable of circumventing geographic barriers and dispersing across biomes, although constrained by environmental filtering. The contemporary diversity and distributions of haemosporidian parasites are mainly driven by historical (speciation) and ecological (dispersal) processes, whereas the parasite community assembly is largely governed by host composition and to a lesser extent by environmental conditions.     

LASIK for Spherical Refractive Myopia: Effect of Topographic Astigmatism (Ocular Residual Astigmatism,ORA) on Refractive Outcome

Purpose

In eyes with a preoperative plano refractive cylinder, it would appear that there is no rationale for astigmatic treatment. The aim of this retrospective, cross-sectional data analysis was to determine the amount of topographic astigmatism in refractive plano eyes that results in reduced efficacy after myopic laser in situ keratomileusis (LASIK).

Methods

This study included 267 eyes from 267 consecutive myopic patients with a refractive plano cylinder. Receiver operating characteristic analysis was used to find the cut-off values of preoperative ocular residual astigmatism (= topographic astigmatism) that can best discriminate between groups of efficacy and safety indices in preoperative plano refractive cylinder eyes.

Results

Preoperative ocular residual astigmatism (ORA) (or topographic astigmatism) of ≤0.9 diopters (D) resulted in an efficacy index of at least 0.8 statistically significantly more frequently than eyes with a preoperative ORA of >0.9 D. Eyes with a high ORA preoperatively also had a high ORA postoperatively. Regression analysis showed that each diopter of preoperative ORA reduced efficacy by 0.07.

Conclusion

A preoperative corneal astigmatism of ≥0.9 D could (partially) be taken into account in the LASIK design, even if the subjective refractive astigmatism is neutral.     

eQTL mapping using allele-specific count data is computationally feasible,powerful, and provides individual-specific estimates of genetic effects

Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP, a computationally efficient method to estimate permutation p-values, which makes it computationally feasible to perform eQTL mapping with ASE counts for large cohorts. We have applied geoP to map eQTLs in 28 human tissues using the data from the Genotype-Tissue Expression (GTEx) project. We demonstrate that using ASE data not only substantially improve the power to detect eQTLs, but also allow us to quantify individual-specific genetic effects, which can be used to study the variation of eQTL effect sizes with respect to other covariates. We also compared two popular methods for eQTL mapping with ASE: TReCASE and RASQUAL. TReCASE is ten times or more faster than RASQUAL and it provides more robust type I error control.     

Ultrastructure of the spermatozoon of the digenean Plagiorchis elegans (Rudolphi, 1802) (Plagiorchioidea,Plagiorchiidae)

The ultrastructure of the mature spermatozoon of the type genus of the Plagiorchiidae Plagiorchis elegans (Rudolphi, 1802), a parasite of the Golden hamster, Mesocricetus auratus is described. This study is the first ultrastructural study of the spermatozoon of a Plagiorchis, the second of a plagiorchiid species and only the third in the Plagiorchioidea. Previously data on spermatozoon ultrastructure existed only for the plagiorchiid Enodiotrema reductum and the omphalometrid Rubenstrema exasperatum. The mature spermatozoon of P. elegans exhibited the general pattern described in most digenean species, namely two axonemes of the 9 + “1” Trepaxonemata pattern, nucleus, mitochondria, external ornamentation of the plasma membrane, spine‐like bodies, and glycogen granules. However, the rather typical expansion of the plasma membrane is not found in P. elegans. Another peculiarity of the spermatozoon of P. elegans is the presence of a structure called thin cytoplasm termination. Spermatozoon ultrastructure of P. elegans is compared with that of E. reductum and R. exasperatum. Spermatozoon of P. elegans conforms to the general pattern described in E. reductum. Thus, this study further expands our knowledge on the spermatozoon ultrastructure among the members of the Plagiorchioidea, one of the most phylogenetically derived groups of the digenea. J. Morphol. 274:965–972, 2013. © 2013 Wiley Periodicals, Inc.     

Developmental microRNA expression profiling of murine embryonic orofacial tissue

BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio‐temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. METHODS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) ‐12, ‐13 and ‐14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real‐time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. RESULTS: Expression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD‐12–GD‐14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters wereshown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial‐mesenchymal transformation, all processes critical for normal orofacial development. CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein‐encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. Birth Defects Research (Part A), 2010. © 2010 Wiley‐Liss, Inc.     

Immobilization of pancreatic lipase on chitin and chitosan

In this study, porcine pancreatic lipase (EC 3.1.1.3) was immobilized on chitin and chitosan by adsorption and subsequent crosslinking with glutaraldehyde, which was added before (conjugation) or after (crosslinking) washing unbound proteins. Conjugation proved to be the better method for both supports. The properties of free and immobilized enzymes were also investigated and compared. The results showed that the pH optimum was shifted from 8.5 to 9.0 for both the immobilized enzymes. Also, the optimum temperature was shifted from 30 to 40 degrees C for chitin-enzyme and to 45 degrees C for chitosan-enzyme conjugates. The immobilization efficiency is low, but the immobilized enzymes have good reusability and stability (storage and operational). Besides these properties, the immobilized lipases were also suitable for catalyzing esterification reactions of fatty acids and fatty alcohols, both with a medium chain length. According to our results, esterification activities of immobilized lipases were two- and four-fold higher for chitosan- and chitin-enzyme, than for the free enzyme, respectively. The immobilization procedure shows a great potential for commercial applications of the immobilized lipase, a relatively low cost commercial enzyme.     

Phylogeny and taxonomy of powdery mildew fungi of Erysiphe sect. Uncinula on Carpinus species

A phylogenetic analysis of the Erysiphe with uncinuloid ascoma appendages (Erysiphe section Uncinula, Erysiphales, Ascomycota) on Carpinus spp. was done using sequences of the rDNA ITS regions and the D1/D2 domains of the 28S rDNA. These results, combined with morphological data, revealed a complex consisting of several distinct taxa. These included the already described Erysiphe carpinicola on C. japonica distinguishable from the Erysiphe sp. on C. betulus and C. tschonoskii as well as the one on C. laxiflora. Thus, it was shown that Oidium carpini, described from Europe on Carpinus betulus, the powdery mildew with uncinula-like ascomata, recently found in Europe on this host, as well as an Erysiphe on C. tschonoskii in Japan, described previously as E. carpinicola, all belong to a single new species, named E. arcuata in this paper. As the powdery mildew on C. laxiflora was also distinct from other known species, it is named E. carpini-laxiflorae in this paper. The already described E. pseudocarpinicola and Erysiphe sp. on Carpinus cordata are two additional taxa, which are morphologically and genetically distinguished from the other species of Erysiphe sect. Uncinula on Carpinus spp.     

Morphological and molecular differentiation of two new species of Pseudoacanthocephalus Petrochenko, 1958 (Acanthocephala: Echinorhynchidae) from amphibians and reptiles in the Philippines, with identification key for the genus

The genus Pseudoacanthocephalus Petrochenko, 1958 currently includes 14 species of acanthocephalans parasitic in amphibians and reptiles worldwide. This work describes two new species of Pseudoacanthocephalus from amphibians and reptiles collected in several localities on Luzon Island, Philippines. Pseudoacanthocephalus nickoli n. sp. was found in two species of frogs, Rana luzonensis Boulenger and Rana similis (Günther), and Pseudoacanthocephalus smalesi n. sp. was found in a scincid lizard, Sphenomorphus abdictus Brown & Alcala. Differential diagnoses of the two new species of Pseudoacanthocephalus from their congeners are provided. Comparative analysis of nuclear ribosomal rRNA sequences encompassing the 3′ end of 18S nuclear rDNA gene, internal transcribed spacer region (ITS1+5.8S+ITS2), and 5′ end of the 28S gene strongly corroborated the morphological evidence and demonstrated significant differences between the two new species as well as between these species and closely related species from continental China and Vietnam. No intraspecific sequence variability was detected among different individuals representing each of the examined species. This is the first report of Pseudoacanthocephalus in the Philippines. A key to known species of Pseudoacanthocephalus is provided.     

Description of a new species of Kurilonema (Nematoda: Rhabdiasidae) from lungs of the skink Sphenomorphus abdictus aquilonius (Reptilia: Squamata: Scincidae) in the Philippines

Kurilonema browni n. sp. is described on the basis of specimens found in the lungs of the scincid lizard Sphenomorphus abdictus aquilonius from Aurora Province, Luzon Island, Philippines. The new species differs from Kurilonema markovi, the only previously known species in the genus, by the presence of 2 prominent lateral pseudolabia, larger body size, shorter tail length relative to total body length, and more numerous eggs in the uteri, containing fully developed larvae. The inner surface of the buccal capsule in the new species is densely covered with rounded scales that have not been observed in K. markovi or any other rhabdiasid species. This is the first record of the genus from the Philippines.     

Meta analysis of Chronic Fatigue Syndrome through integration of clinical, gene expression, SNP and proteomic data

The histone octamer induced bending of DNA into the super-helix structure in nucleosome core particle, is very unique and vital for DNA packing into chromatin. We collected 48 nucleosome crystal structures from PDB and applied a multivariate analysis on the nucleosome structural data. Based on the anisotropic nature of DNA structure, a principal conformational subspace (PCS) is derived from multiple properties to represent the most significant variances of nucleosome DNA structures. The coupling of base pair-oriented parameters with sugar phosphate backbone parameters presented in principal dimensionalities reveals two main deformation modes that have supplemented the existing physical model. By using sequence alignment-based statistics, a positiondependent conformational map for the super-helical DNA path is established. The result shows that the crystal structures of nucleosome DNA have much consistency in position-specific structural variations and certain periodicity is found to exist in these variations. Thus, the positions with obvious deformation patterns along the DNA path in nucleosome core particle are relatively conservative from the perspective of statistics.