A review of techniques for spatial modeling in geographical, conservation and landscape genetics

Most evolutionary processes occur in a spatial context and several spatial analysis techniques have been employed in an exploratory context. However, the existence of autocorrelation can also perturb significance tests when data is analyzed using standard correlation and regression techniques on modeling genetic data as a function of explanatory variables. In this case, more complex models incorporating the effects of autocorrelation must be used. Here we review those models and compared their relative performances in a simple simulation, in which spatial patterns in allele frequencies were generated by a balance between random variation within populations and spatially-structured gene flow. Notwithstanding the somewhat idiosyncratic behavior of the techniques evaluated, it is clear that spatial autocorrelation affects Type I errors and that standard linear regression does not provide minimum variance estimators. Due to its flexibility, we stress that principal coordinate of neighbor matrices (PCNM) and related eigenvector mapping techniques seem to be the best approaches to spatial regression. In general, we hope that our review of commonly used spatial regression techniques in biology and ecology may aid population geneticists towards providing better explanations for population structures dealing with more complex regression problems throughout geographic space

Phase I/II Trial of Liver-derived Mesenchymal Stem Cells in Pediatric Liver-based Metabolic Disorders: A Prospective, Open Label, Multicenter, Partially Randomized, Safety Study of One Cycle of Heterologous Human Adult Liver-derived Progenitor Cells (HepaStem) in Urea Cycle Disorders and Crigler-Najjar Syndrome Patients

Background. Regenerative medicine using stem cell technology is an emerging field that is currently tested for inborn and acquired liver diseases. Objective. This phase I/II prospective, open label, multicenter, randomized trial aimed primarily at evaluating the safety of Heterologous Human Adult Liver–derived Progenitor Cells (HepaStem) in pediatric patients with urea cycle disorders (UCDs) or Crigler-Najjar (CN) syndrome 6 months posttransplantation. The secondary objective included the assessment of safety up to 12 months postinfusion and of preliminary efficacy. Methods. Fourteen patients with UCDs and 6 with CN syndrome were divided into 3 cohorts by body weight and intraportally infused with 3 doses of HepaStem. Clinical status, portal vein hemodynamics, morphology of the liver, de novo detection of circulating anti–human leukocyte antigen antibodies, and clinically significant adverse events (AEs) and serious adverse events to infusion were evaluated by using an intent-to-treat analysis. Results. The overall safety of HepaStem was confirmed. For the entire study period, patient-month incidence rate was 1.76 for the AEs and 0.21 for the serious adverse events, of which 38% occurred within 1 month postinfusion. There was a trend of higher events in UCD as compared with CN patients. Segmental left portal vein thrombosis occurred in 1 patient and intraluminal local transient thrombus in a second patient. The other AEs were in line with expectations for catheter placement, cell infusion, concomitant medications, age, and underlying diseases. Conclusions. This study led to European clinical trial authorization for a phase II study in a homogeneous patient cohort, with repeated infusions and intermediate doses

Recruitment Potential of a Green Alga Ulva flexuosa Wulfen Dark Preserved Zoospore and Its Development

The recruitment potential and the ability of Ulva flexuosa Wulfen zoospores to survive darkness were tested under different conditions in the present study. The dark preserved zoospore was cultured under a two-factor experimental design to test the effect of salinity and nitrate, effect of salinity and phosphate, effect of light and salinity, and effect of light and phosphate. The recruitment (germination and growth) of zoospores was significantly affected by light and salinity. The nitrate concentration of 20 µmol.l−1 was found to initiate the process of germination and its subsequent growth and, its effect appeared greatest under 25 psu condition. While nitrate enhances the growth of biomass more than phosphate, both show a positive interactive effect on biomass increase when crossed with salinity. The combined effect of 25 psu salinity and 8 µmol.l−1 phosphate exhibited higher biomass growth. There was a significant effect of light and salinity on the biomass of zoospore, though there was no significant interaction between the two factors. There was an increase in biomass of growing zoospores to increase in light intensity and 80 µmol.m−2.s−1 of light intensity was considered optimal. Similarly, high light intensity condition favored higher biomass growth and there was significant interaction between light (80 µmol. m−2. s−1) and phosphate (4 µmol. l−1) in high salinity (35 psu) condition. The result of this study showed that dark preserved zoospores of U. flexuosa have the potential for recruitment and it gives us an understanding how different factors play a role in the process of recruitment

Analysis of sexual phenotype and prezygotic fertility in natural populations of Fucus spiralis, F. vesiculosus (Fucaceae, Phaeophyceae) and their putative hybrids

In the genus Fucus, the character dioecy/hermaphroditism has undergone multiple state changes and hybridization is possible between taxa with contrasting mating systems, e.g. between the dioecious Fucus vesiculosus and the hermaphrodite F. spiralis. In the context of mating system evolution, we evaluated the potential consequences of hybridization by studying the variation in sexual phenotype and prezygotic fertility. Firstly, as a result of hybridization between the two sexual systems, gender variation may arise depending on the relative importance of genes with large versus small phenotypic effects. We thus qualitatively examined the extent of gender variation within and among individual hybrids in comparison with both parental species. Secondly, if hybridization breaks up co-adapted gene complexes, hybrid fertility may be reduced in comparison with both parental species. Therefore, we also quantified male and female prezygotic fertility in parental species and their hybrids in order to test for reduction in hybrid fitness. A total of 89 sexually mature individuals (20 F. spiralis, 40 F. vesiculosus, 10 hermaphrodite hybrids and 19 dioecious hybrids) were sampled in two geographically distant regions (France and Portugal) and six conceptacles per individual were observed. Within-individual variation was very restricted qualitatively – only one hybrid carried a conceptacle with a different sexual phenotype from the five others – as well as quantitatively. This suggests a simple genetic system for sex determination involving a few genes with major effects. In addition, analyses showed no significant decrease in hybrid fertility compared with parental species. Moreover, hybrids exhibited all sexual phenotypes, suggesting several generations of hybridization and backcrossing and, therefore, that hybrids are reproductively successful. Finally, the occurrence of sterile paraphyses in female and hermaphrodite individuals was interpreted as a relic of male function and suggests that, as in higher plants, evolution from hermaphroditism to dioecy may be the most parsimonious pathway

Humoral immune response and delayed type hypersensitivity to influenza vaccine in patients with diabetes mellitus

The antibody response and delayed type hypersensitivity reaction to commercially available trivalent influenza vaccine in 159 patients with diabetes mellitus was compared with response and reaction in 28 healthy volunteers. A correction for prevaccination titres was made. No differences were found between diabetic patients and control subjects with respect to antibody response to the three vaccine strains as measured by the difference between geometric mean titres of post- and prevaccination sera. In Type 1 (insulin-dependent) diabetic patients the incidence of non-responders to two vaccine components was significantly increased (p less than 0.05). The delayed type hypersensitivity reaction to influenza antigen was significantly decreased in patients with high concentrations of glycosylated haemoglobin (p less than 0.01). These findings suggest a role for impaired immune response in the increased influenza morbidity and mortality in patients with diabetes mellitus. Implications for therapy and vaccination strategy are discussed

Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions

<p>Abstract</p> <p>Background</p> <p>Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be the result of single points of failure but instead likely arise from the joint failure of two or more interacting components. The hope in genome-wide screens is that these points of failure can be linked to single nucleotide polymorphisms (SNPs) which confer disease susceptibility. Detecting interacting variants that lead to disease in the absence of single-gene effects is difficult however, and methods to exhaustively analyze sets of these variants for interactions are combinatorial in nature thus making them computationally infeasible. Efficient algorithms which can detect interacting SNPs are needed. ReliefF is one such promising algorithm, although it has low success rate for noisy datasets when the interaction effect is small. ReliefF has been paired with an iterative approach, Tuned ReliefF (TuRF), which improves the estimation of weights in noisy data but does not fundamentally change the underlying ReliefF algorithm. To improve the sensitivity of studies using these methods to detect small effects we introduce Spatially Uniform ReliefF (SURF).</p> <p>Results</p> <p>SURF's ability to detect interactions in this domain is significantly greater than that of ReliefF. Similarly SURF, in combination with the TuRF strategy significantly outperforms TuRF alone for SNP selection under an epistasis model. It is important to note that this success rate increase does not require an increase in algorithmic complexity and allows for increased success rate, even with the removal of a nuisance parameter from the algorithm.</p> <p>Conclusion</p> <p>Researchers performing genetic association studies and aiming to discover gene-gene interactions associated with increased disease susceptibility should use SURF in place of ReliefF. For instance, SURF should be used instead of ReliefF to filter a dataset before an exhaustive MDR analysis. This change increases the ability of a study to detect gene-gene interactions. The SURF algorithm is implemented in the open source Multifactor Dimensionality Reduction (MDR) software package available from <url>http://www.epistasis.org</url>.</p

Assessment of Attractiveness of Plants as Roosting Sites for the Melon Fly, Bactrocera cucurbitae, and Oriental Fruit Fly, Bactrocera dorsalis

The use of toxic protein bait sprays to suppress melon fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), populations typically involves application to vegetation bordering agricultural host areas where the adults seek shelter (“roost”). Although bait spray applications for suppression of oriental fruit fly, Bactrocera dorsalis (Hendel), populations have traditionally been applied to the host crop, rather than to crop borders, roosting by oriental fruit flies in borders of some crop species, such as papaya, Carica papaya L. (Brassicales: Caricaceae), suggests that bait spray applications to crop borders could also help in suppression of B. dorsalis populations. In order to develop improved recommendations for application of bait sprays to border plants for suppression of melon fly and oriental fruit fly populations, the relative attractiveness of a range of plant species, in a vegetative (non-flowering) stage, was tested to wild melon fly and oriental fruit fly populations established in a papaya orchard in Hawaii. A total of 20 plant species were evaluated, divided into four categories: 1) border plants, including corn, Zea mays L. (Poales: Poaceae), windbreaks and broad-leaved ornamentals, 7 species; 2) weed plants commonly found in agricultural fields in Hawaii, 6 species; 3) host crop plants, 1 species- zucchini, Cucurbita pepo L. (Violales: Curcurbitaceae), and 4) locally grown fruit trees, 6 species. Plants were established in pots and placed in an open field, in clusters encircling protein bait traps, 20 m away from the papaya orchard. Castor bean, Ricinus communis L. (Euphorbiales: Euphorbiaceae), panax, Polyscias guilfoylei (Bull) Bailey (Apiales: Araliaceae), tiger's claw, Erythnna variegata L. (Fabales: Fabaceae), and guava, Psidium guajava L. (Myrtales: Myrtaceae) were identified as preferred roosting hosts for the melon fly, and tiger's claw, panax, castor bean, Canada cocklebur, Xanthium strumarium L. (Asterales: Asteraceae), Brazilian pepper tree, Schinus terebinthifolius Raddi (Sapindales: Anacardiaceae), ti plant, Cordyline terminate (L.) Chev.(Liliales: Liliaceae), guava and several Citrus spp. were identified as preferred roosting hosts for oriental fruit fly. Guava had not previously been identified as a preferred roosting host for melon fly. Other than for the use of panax as a roosting host, there has previously been little attention to roosting hosts for oriental fruit fly. Establishment of preferred roosting hosts as crop borders may help to improve suppression of both fruit fly species by providing sites for bait spray applications. Further research is needed to assess the use of vegetation bordering other host crops as roosting hosts, especially for oriental fruit fly

Small-Bodied Humans from Palau, Micronesia

UNLABELLED: Newly discovered fossil assemblages of small bodied Homo sapiens from Palau, Micronesia possess characters thought to be taxonomically primitive for the genus Homo. BACKGROUND: Recent surface collection and test excavation in limestone caves in the rock islands of Palau, Micronesia, has produced a sizeable sample of human skeletal remains dating roughly between 940-2890 cal ybp. PRINCIPLE FINDINGS: Preliminary analysis indicates that this material is important for two reasons. First, individuals from the older time horizons are small in body size even relative to "pygmoid" populations from Southeast Asia and Indonesia, and thus may represent a marked case of human insular dwarfism. Second, while possessing a number of derived features that align them with Homo sapiens, the human remains from Palau also exhibit several skeletal traits that are considered to be primitive for the genus Homo. SIGNIFICANCE: These features may be previously unrecognized developmental correlates of small body size and, if so, they may have important implications for interpreting the taxonomic affinities of fossil specimens of Homo

Crayfish Recognize the Faces of Fight Opponents

The capacity to associate stimuli underlies many cognitive abilities, including recognition, in humans and other animals. Vertebrates process different categories of information separately and then reassemble the distilled information for unique identification, storage and recall. Invertebrates have fewer neural networks and fewer neural processing options so study of their behavior may reveal underlying mechanisms still not fully understood for any animal. Some invertebrates form complex social colonies and are capable of visual memory–bees and wasps, for example. This ability would not be predicted in species that interact in random pairs without strong social cohesion; for example, crayfish. They have chemical memory but the extent to which they remember visual features is unknown. Here we demonstrate that the crayfish Cherax destructor is capable of visual recognition of individuals. The simplicity of their interactions allowed us to examine the behavior and some characteristics of the visual features involved. We showed that facial features are learned during face-to-face fights, that highly variable cues are used, that the type of variability is important, and that the learning is context-dependent. We also tested whether it is possible to engineer false identifications and for animals to distinguish between twin opponents

Marsh macrophyte responses to inundation anticipate impacts of sea-level rise and indicate ongoing drowning of North Carolina marshes

In situ persistence of coastal marsh habitat as sea level rises depends on whether macrophytes induce compensatory accretion of the marsh surface. Experimental planters in two North Carolina marshes served to expose two dominant macrophyte species to six different elevations spanning 0.75 m (inundation durations 0.4–99 %). Spartina alterniflora and Juncus roemerianus exhibited similar responses—with production in planters suggesting initial increases and then demonstrating subsequent steep declines with increasing inundation, conforming to a segment of the ecophysiological parabola. Projecting inundation levels experienced by macrophytes in the planters onto adjacent marsh platforms revealed that neither species occupied elevations associated with increasing production. Declining macrophyte production with rising seas reduces both bioaccumulation of roots below-ground and baffle-induced sedimentation above-ground. By occupying only descending portions of the parabola, macrophytes in central North Carolina marshes are responding to rising water levels by progressive declines in production, ultimately leading to marsh drowning