Genomic selection prediction models comparing sequence capture and SNP array genotyping methods

The successful application of genomic selection (GS) approaches is dependent on genetic makers derived from high-throughput and low-cost genotyping methods. Recent GS studies in trees have predominantly relied on SNP arrays as the source of genotyping, though this technology has a high entry cost. The recent development of alternative genotyping platforms, tailored to specific species and with low entry cost, has become possible due to advances in next-generation sequencing and genome complexity reduction methods such as sequence capture. However, the performance of these new platforms in GS models has not yet been evaluated, or compared to models developed from SNP arrays. Here, we evaluate the impact of these genotyping technologies on the development of GS prediction models for a Eucalyptus breeding population composed of 739 trees phenotyped for 13 wood quality and growth traits. Genotyping data obtained with both methods were compared for linkage disequilibrium, minor allele frequency, and missing data. Phenotypic prediction methods RR-BLUP and BayesB were employed, while predictive ability using cross validation was used to evaluate the performance of GS models derived from the different genotyping platforms. Differences in linkage disequilibrium patterns, minor allele frequency, missing data, and marker distribution were detected between sequence capture and SNP arrays. However, RR-BLUP and BayesB GS models resulted in similar predictive abilities. These results demonstrate that both genotyping methods are equivalent for genomic prediction of the traits evaluated. Sequence capture offers an alternative for species where SNP arrays are not available, or for when the initial development cost is too high.     

Insects Associated with Pig Carrion in Two Environments of the Brazilian Savanna

Studies of carrion fauna have increased in Brazil and have contributed to the knowledge of this fauna in the national territory. Brazil has continental dimensions and presents various biomes in its territorial area. Most of the carrion fauna have seldom been studied, and this is especially true for the Savanna or “Cerrado.” The present research examined the fauna visiting carrion in two environments and two seasons in a rural area situated in a region of Cerrado in southeastern Brazil. The two environments studied were a pasture and a fragment of semi-deciduous forest. Samples were collected during the dry and humid seasons of the year. The study identified the diversity and relative abundance of species attracted to pig carcasses (Sus scrofa L.) exposed in each environment and season. Eight pig carcasses (10 ± 1 kg) were placed in traps, and adult insects attracted to the traps were collected during the decay of the carcasses. A total of 92,489 insects were collected during the experiments. The Diptera was the most frequent order (92.2%) represented by 27 families and at least 124 species. This was followed by Coleoptera (4.4%) represented by 14 families and at least 65 species. Sarcophagidae had the greatest diversity of species, followed by Muscidae and Calliphoridae. Several species were collected only during a specific period of the year or in a single environment. The results are important from an ecological point of view and for Medico-Legal Forensic Entomology.     

Morphology and development of the male reproductive tract in Callinectes danae (Crustacea: Brachyura)

The aim of this study was to characterize the morphology and function of each section of the reproductive system of male Callinectes danae, as well as the stages of reproductive development and their relation to secondary sexual characteristics. Development of their reproductive system begins after completion of the pubertal moult. The growth of the gonopodium showed negative allometry for both juveniles and adults. The reproductive system is divided into portions with different functions. There is a germinal zone in the testes containing spermatogonia, a zone of maturation containing spermatocytes, spermatids or spermatozoa, as well as a collecting duct, which carries spermatozoa to the vas deferens. There are two matrices in the anterior vas deferens that initiate the separation of spermatozoa groups, one composed of polysaccharide acids (matrix I) and another consisting of neutral polysaccharides (matrix II). In the median vas deferens, the matrix II forms an acellular capsule, which forms the spermatophores. In the posterior vas deferens, the matrices are accumulated, initially with a granular texture and are homogenous for the final portion. The ejaculatory duct and penis have muscle lining to expel the spermatophores at copulation. Even after copulation, males retain a stock of spermatophores, allowing copulation with other females.     

Neonatal Immune Challenge with Lipopolysaccharide Triggers Long-lasting Sex- and Age-related Behavioral and Immune/Neurotrophic Alterations in Mice: Relevance to Autism Spectrum Disorders

Early-life challenges, particularly infections and stress, are related to neuropsychiatric disorders such as autism and schizophrenia. Here, we conducted a wide range of behavioral tests in periadolescent (postnatal day (PN) 35) and adult (PN70) Swiss mice neonatally challenged with LPS on PN5 and -7, to unveil behavioral alterations triggered by LPS exposure. Immune and neurotrophic (brain-derived neurotrophic factor—BDNF) alterations were determined in the prefrontal cortex (PFC), hippocampus (HC), and hypothalamus (HT). Since the incidence and clinical manifestations of neurodevelopmental disorders present significant sex-related differences, we sought to distinctly evaluate male and female mice. While on PN35, LPS-challenged male mice presented depressive, anxiety-like, repetitive behavior, and working memory deficits; on PN70, only depressive- and anxiety-like behaviors were observed. Conversely, females presented prepulse inhibition (PPI) deficits in both ages studied. Behavioral changes in periadolescence and adulthood were accompanied, in both sexes, by increased levels of interleukin (IL-4) (PFC, HC, and HT) and decreased levels of IL-6 (PFC, HC, and HT). BDNF levels increased in both sexes on PN70. LPS-challenged male mice presented, in both ages evaluated, increased HC myeloperoxidase activity (MPO); while when adult increased levels of interferon gamma (IFNγ), nitrite and decreased parvalbumin were observed. Alterations in innate immunity and parvalbumin were the main LPS-induced remarks between males and females in our study. We concluded that neonatal LPS challenge triggers sex-specific behavioral and neurochemical alterations that resemble autism spectrum disorder, constituting in a relevant model for the mechanistic investigation of sex bias associated with the development of this disorder.     

<Emphasis Type="Italic">MBL2</Emphasis> gene polymorphisms in HHV-8 infection in people living with HIV/AIDS

Background

Host genetic factors such as MBL2 gene polymorphisms cause defects in the polymerization of MBL protein and result in a functional deficiency and/or in low serum levels that can influence susceptibility to various viral infections. The aim of this study was to estimate the frequency of alleles, genotypes and haplotypes related to -550, -221 and exon 1 polymorphisms of the MBL2 gene and investigate their association with HHV-8 in people living with HIV/AIDS (PLWHA), as well as the impacts on CD4 cell count and HIV viral load in HIV/HHV-8 coinfected and HIV monoinfected patients.

Results

A cross sectional study in PLWHA, with and without HHV-8 infection, exploring associations between different factors, was performed in the outpatient infectious and parasitic diseases clinic at a referral hospital. Genomic DNA extractions from leukocytes were performed using a commercial Wizard^® Genomic DNA Purification kit (Promega, Madison, WI). The promoter region (-550 and -221) was genotyped with the TaqMan system (Applied TaqMan Biosystems^® genotyping Assays), and the structural region (exon1) was genotyped with Express Sybr Greener Supermix kit (Invitrogen, USA). In total, 124 HIV/HHV-8 coinfected and 213 HIV monoinfected patients were analysed. Median TCD4 counts were significantly lower in HIV/HHV-8 coinfected patients, whereas the mean of the first and last viral load of HIV did not present significant difference. There was no difference in frequency between the LL, YY and AA genotypes between the HIV/HHV-8 coinfected or HIV monoinfected patients. However, in a multivariate analysis, coinfected patients with the intermediate expression haplotype of the MBL2 gene had an odds ratio of 3.1-fold (CI?=?1.2–7.6) of their last CD4 cell count being below 350 cells/mm³. Among the coinfected individuals, four developed KS and presented the intermediate expression MBL haplotype, with three being HYA/LXA and one being LYA/LYO.

Conclusions

Host genetic factors, such as -550, -221 and exon 1 polymorphisms, can be related to the may modify coinfections and/or to the development clinical manifestations caused by HHV-8, especially in HIV/HHV-8 coinfected patients who present the intermediate expression haplotypes of MBL.

     

Breeding plumage honestly signals likelihood of tapeworm infestation in females of a long-distance migrating shorebird, the bar-tailed godwit

The indicator mechanism for sexual selection proposed by Hamilton and Zuk (i.e. that sexually selected ornaments signal parasite resistance) has received rather little observational support, and none in the case of long-distance migrant birds. Here we present a test by examining the association between helminth infestations and breeding plumage quality in bar-tailed godwits Limosa lapponica taymyrensis during their spring staging period in the Wadden Sea, The Netherlands. After a non-stop flight from West Africa, these shorebirds refuel in the Wadden Sea in preparation for a second flight to the central Siberian Arctic breeding grounds. Earlier studies have shown that only relatively heavy and well ornamented birds carry out a "top-up" moult during stopover, in which part of the contour feathers recently grown in West Africa are replaced by even fresher ones. Active body moult was therefore taken as the primary indicator of ornament quality. Of 78 birds collected between 1992 and 1997, 42% carried helminths, including four species of digenean trematodes (flukes), three species of cestodes (tapeworms) and an acanthocephalan (spiny-headed worm). Faecal samples examined for helminth eggs in another 92 birds in 1998 and 2000 showed similar rates of infestation. Actively moulting bar-tailed godwits were confirmed to be heavier and to show more extensive breeding plumage than non-moulting birds. In females, but not in males, active moult was associated with fewer cestodes and acanthocephalans. Also, breeding plumage and presence of cestodes were negatively associated in females. We argue that the quality of the breeding plumage reliably indicates parasite resistance in female godwits. The repeatability of plumage scores of females between years is consistent with such resistance having a heritable component. In contrast, male ornaments may demonstrate other qualities, e.g. an ability to combine adequate fuelling and flight performances with moult during the time-stress of migration.     

Scale-Adjusted Metrics for Predicting the Evolution of Urban Indicators and Quantifying the Performance of Cities

More than a half of world population is now living in cities and this number is expected to be two-thirds by 2050. Fostered by the relevancy of a scientific characterization of cities and for the availability of an unprecedented amount of data, academics have recently immersed in this topic and one of the most striking and universal finding was the discovery of robust allometric scaling laws between several urban indicators and the population size. Despite that, most governmental reports and several academic works still ignore these nonlinearities by often analyzing the raw or the per capita value of urban indicators, a practice that actually makes the urban metrics biased towards small or large cities depending on whether we have super or sublinear allometries. By following the ideas of Bettencourt et al. [PLoS ONE 5 (2010) e13541], we account for this bias by evaluating the difference between the actual value of an urban indicator and the value expected by the allometry with the population size. We show that this scale-adjusted metric provides a more appropriate/informative summary of the evolution of urban indicators and reveals patterns that do not appear in the evolution of per capita values of indicators obtained from Brazilian cities. We also show that these scale-adjusted metrics are strongly correlated with their past values by a linear correspondence and that they also display crosscorrelations among themselves. Simple linear models account for 31%–97% of the observed variance in data and correctly reproduce the average of the scale-adjusted metric when grouping the cities in above and below the allometric laws. We further employ these models to forecast future values of urban indicators and, by visualizing the predicted changes, we verify the emergence of spatial clusters characterized by regions of the Brazilian territory where we expect an increase or a decrease in the values of urban indicators.     

Specificity of the local transfer of cell-mediated immunity with dialyzable transfer factor

Local transfer of delayed cutaneous reactions to PPD, candidin, streptokinase-streptodornase, and leishmanin was used to study the specificity of dialyzable transfer factor (TF). Whereas conversions of reactions that were negative in the donors were achieved in experiments using the ubiquitous antigens, transfer of sensitivity to leishmanin (Montenegro reaction) was only accomplished by using TF of Montenegro-positive individuals. It was concluded that TF has specific properties and that ubiquitous antigens are not suitable for studying the specificity of the transfer, since the possibility of presensitization of the donors cannot be excluded in spite of negative cutaneous reaction.     

The impact of tropical forest logging and oil palm agriculture on the soil microbiome

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land‐use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once‐logged and twice‐logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell–cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land‐use changes on the interaction of soil microbes.