Double‐digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird

Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150–600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade‐offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy‐wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD‐seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost‐ and time‐efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated.     

Distribution of hepatic phosphofructokinase isozymes in parenchymal and sinusoidal cells.

The distribution profile of the isozymes of phosphofructokinase (PFK) in different cell types of rat liver is established using the techniques of electrophoresis and immunodiffusion. Agarose gel electrophoresis of the extracts of parenchymal cells, Kupffer or sinusoidal cells, and whole liver indicated that two PFK isozymes are present in whole liver and that the faster moving hepatic PFK isozyme is present only in parenchymal cells; whereas, the slower moving hepatic PFK isozyme is only in sinusoidal cells. Immunodiffusion studies using antiserum specific for the major hepatic PFK isozyme (PFK-L₂) revealed that PFK-L₂ is present only in whole liver or parenchymal cell extracts and is absent from sinusoidal cells. It is apparent that the other hepatic PFK isozyme (PFK-L₁) is normally found only in sinusoidal cells.     

Real-time definition of non-randomness in the distribution of genomic events

Features such as mutations or structural characteristics can be non-randomly or non-uniformly distributed within a genome. So far, computer simulations were required for statistical inferences on the distribution of sequence motifs. Here, we show that these analyses are possible using an analytical, mathematical approach. For the assessment of non-randomness, our calculations only require information including genome size, number of (sampled) sequence motifs and distance parameters. We have developed computer programs evaluating our analytical formulas for the real-time determination of expected values and p-values. This approach permits a flexible cluster definition that can be applied to most effectively identify non-random or non-uniform sequence motif distribution. As an example, we show the effectivity and reliability of our mathematical approach in clinical retroviral vector integration site distribution.     

Low molecular weight catalytic metalloporphyrin antioxidant AEOL 10150 protects lungs from fractionated radiation

The objective of this study was to determine whether administration of a catalytic antioxidant, Mn(III) tetrakis(N,N'-diethylimidazolium-2-yl) porphyrin, AEOL10150, reduces the severity of long-term lung injury induced by fractionated radiation (RT). Fisher 344 rats were randomized into five groups: RT+AEOL10150 (2.5 mg/kg BID), AEOL10150 (2.5 mg/kg BID) alone, RT+ AEOL10150 (5 mg/kg BID), AEOL10150 (5 mg/kg BID) alone and RT alone. Animals received five 8 Gy fractions of RT to the right hemithorax. AEOL10150 was administered 15 min before RT and 8 h later during the period of RT treatment (5 days), followed by subcutaneous injections for 30 days, twice daily. Lung histology at 26 weeks revealed a significant decrease in lung structural damage and collagen deposition in RT+AEOL10150 (5 mg/kg BID) group, in comparison to RT alone. Immunohistochemistry studies revealed a significant reduction in tissue hypoxia (HIF1alpha, CAIX), angiogenic response (VEGF, CD-31), inflammation (ED-1), oxidative stress (8-OHdG, 3-nitrotyrosine) and fibrosis pathway (TGFbeta1, Smad3, p-Smad2/3), in animals receiving RT+ AEOL10150 (5 mg/kg BID). Administration of AEOL10150 at 5 mg/kg BID during and after RT results in a significant protective effect from long-term RT-induced lung injury. Low dose (2.5 mg/kg BID) delivery of AEOL10150 has no beneficial radioprotective effects.     

Multiple hypotheses explain variation in extra‐pair paternity at different levels in a single bird family

Extra‐pair paternity (EPP), where offspring are sired by a male other than the social male, varies enormously both within and among species. Trying to explain this variation has proved difficult because the majority of the interspecific variation is phylogenetically based. Ideally, variation in EPP should be investigated in closely related species, but clades with sufficient variation are rare. We present a comprehensive multifactorial test to explain variation in EPP among individuals in 20 populations of nine species over 89 years from a single bird family (Maluridae). Females had higher EPP in the presence of more helpers, more neighbours or if paired incestuously. Furthermore, higher EPP occurred in years with many incestuous pairs, populations with many helpers and species with high male density or in which males provide less care. Altogether, these variables accounted for 48% of the total and 89% of the interspecific and interpopulation variation in EPP. These findings indicate why consistent patterns in EPP have been so challenging to detect and suggest that a single predictor is unlikely to account for the enormous variation in EPP across levels of analysis. Nevertheless, it also shows that existing hypotheses can explain the variation in EPP well and that the density of males in particular is a good predictor to explain variation in EPP among species when a large part of the confounding effect of phylogeny is excluded.     

Persistence of native and exotic plants 10 years after prairie reconstruction

Prairie reconstructions are a critical component of preservation of the imperiled tallgrass prairie ecosystem in the Midwestern United States. Sustainability of this endeavor depends on establishment of persistent cover of planted native species and resistance to noxious weeds. The goal of this study was to understand the influence of early reconstruction practices on long‐term outcomes. Twelve replicates of three planting methods (dormant‐season broadcast, growing‐season broadcast, and growing‐season drill) and three seed mix richness levels (10, 20, or 34 species), fully crossed in a completely randomized design were planted in 2005 on nine former agricultural fields located in Iowa and Minnesota. Cover by species was estimated in 2005–2007, 2010, and 2015. In 2015, cover of planted species, native nonplanted species, and exotic species were similar to those recorded in 2010. Cover of the noxious weed Cirsium arvense had also declined by an average of 49% without herbicide from a peak in 2007 to low stable levels from 2010 to 2015. Richness of planted forbs, on the other hand, were still increasing in high‐richness broadcast treatments (e.g. 17–59% increase 2010–1015 in Minnesota). Two results in 2015 are reasons for concern: cover of planted species is only slightly over 50% in both Minnesota and Iowa, though with forbs still increasing, this may improve; and the cool‐season exotic grasses Poa pratensis and Bromus inermis are increasing at both Minnesota and Iowa sites. Control of these invasive grasses will be necessary, but care will be needed to avoid negative impacts of control methods on natives.     

Endocrine components of body fluid homeostasis

1. Linear relationships between plasma osmolality and thirst and vasopressin secretion are described in conscious dogs. 2. During water deprivation, natriuresis occurs which ameliorates the rise in plasma osmolality. 3. Increases in plasma osmolality prevent the stimulation of aldosterone secretion by angiotensin II.     

Prefrontal asymmetry and parent-rated temperament in infants

Indicators of temperament appear early in infancy and remain relatively stable over time. Despite a great deal of interest in biological indices of temperament, most studies of infant temperament rely on parental reports or behavioral tasks. Thus, the extent to which commonly used temperament measures relate to potential biological indicators of infant temperament is still relatively unknown. The current experiment examines the relationship between a common parental report measure of temperament--the Infant Behavior Questionnaire-Revised (IBQ-R)--and measures of frontal EEG asymmetry in infants. We examined associations between the subscales of the IBQ-R and frontal EEG asymmetry scores recorded during a combined series of neutral attentional and putatively emotional recording conditions in infants between 7 and 9 months of age. We predicted that approach-related subscales of the IBQ-R (e.g., Approach, Soothability) would be related to greater left prefrontal asymmetry, while withdrawal-related subscales (e.g., Distress to Limitations, Fear, Falling Reactivity, Perceptual Sensitivity) would be related to greater right prefrontal asymmetry. In the mid- and lateral-frontal regions, Approach, Distress to Limitations, Fear, Soothability, and Perceptual Sensitivity were generally associated with greater left frontal activation (rs≥.23, ps<0.05), while only Falling Reactivity was associated with greater right frontal activation (rs≤-.44, ps<0.05). Results suggest that variability in frontal EEG asymmetry is robustly associated with parental report measures of temperament in infancy.     

Weight loss is not mandatory for exercise-induced effects on health indices in females with metabolic syndrome

The aim of this study was to investigate the impact of moderate aerobic training on functional, anthropometric, biochemical, and health-related quality of life (HRQOL) parameters on women with metabolic syndrome (MS). Fifteen untrained women with MS performed moderate aerobic training for 15 weeks, without modifications of dietary behaviours. Functional, anthropometric, biochemical, control diet record and HRQOL parameters were assessed before and after the training. Despite body weight maintenance, the patients presented decreases in waist circumference (P = 0.001), number of MS components (P = 0.014), total cholesterol (P = 0.049), HDL cholesterol (P = 0.004), LDL cholesterol (P = 0.027), myeloperoxidase activity (P = 0.002) and thiobarbituric acid-reactive substances levels (P = 0.006). There were no differences in total energy, carbohydrate, protein and lipid intake pre- and post-training. Furthermore, improvements in the HRQOL subscales of physical functioning (P = 0.03), role-physical (P = 0.039), bodily pain (P = 0.048), general health (P = 0.046) and social functioning scoring (P = 0.011) were reported. Despite the absence of weight loss, aerobic training induced beneficial effects on functional, anthropometric, biochemical and HRQOL parameters in women with MS.     

Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region

Background

In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP) and sedoheptulose-1, 7-bisphosphate (SBP) are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase), while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase) and sedoheptulose-1, 7-bisphosphatase (SBPase), respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario.

Results

Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II). Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations.

Conclusions

There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins: SBPase share a common ancestor with the gluconeogenesis-specific Class I FBPase of epsilon-proteobacteria (or probably originated from that of the ancestor of epsilon-proteobacteria), while FBPase arise from Class I FBPase of an unknown kind of eubacteria. During the evolution of SBPase from eubacterial Class I FBPase, the SBP-dephosphorylation activity was acquired through the transition ??from specialist to generalist??. The evolutionary substitution of the endosymbiotic-origin cyanobacterial bifunctional F/SBPase by the two light-regulated substrate-specific enzymes made the regulation of the Calvin cycle more delicate, which contributed to the evolution of eukaryotic photosynthesis and even the entire photosynthetic eukaryotes.