Sex-specific associations between reproductive output and hematozoan parasites of American kestrels

Parasites have the potential to decrease reproductive output of hosts by competing for nutrients or forcing hosts to invest in immune function. Conversely, reproductive output may affect parasite loads if hosts allocate resources to reproduction such that allocation to immune function is compromised. Both hypotheses implicitly have a temporal component, so we sampled parasites both before and after egg laying to examine the relationship between reproductive output (indexed using a combined measure of clutch size, egg volume, and initiation date) and blood parasite loads of American kestrels (Falco sparverius). Parasite loads measured prior to egg laying had no adverse effects on subsequent reproductive output. Females that previously had large reproductive outputs subsequently had lower parasite intensities than those whose outputs were smaller, suggesting that females were capable of allocating energy to both forming clutches and reducing parasite loads. Because male kestrels provide most of their mate's energetic needs before, during, and after egg laying, mate choice by females may have consequences for their parasite loads. Females choosing high-quality mates may not only have increased reproductive output, but may also obtain sufficient resources from their mates to enable them to reduce their parasite burdens. Males whose mates had large reproductive outputs were more likely to subsequently be parasitized and have more intense infections. For individual males sampled both before and after egg laying, those whose mates had larger reproductive outputs were also more likely to become parasitized, or remain parasitized, between sampling periods. Increased parasite loads of males may be one mechanism by which the costs of reproduction are paid.     

Depth distribution of cherry (Prunus avium L.) tree roots as influenced by grass root competition

We investigated the effect of competition from grass roots (as controlled by herbicide application) on the depth distribution of white roots in cherry trees, grown with varying rates and frequency of application of N in an agroforestry system. Statistical summaries of distribution, namely mean and skewness, produced a concise and interpretable analysis of the data.There was a large increase in tree root numbers in the surface horizons after the herbicide had reduced grass root competition. Where the surrounding grass had not been reduced by herbicide, the average depth of tree roots increased with time, contrasting with a marked shift in the mode of distribution of root numbers to shallow depths when grass competition was removed. These findings are important in the understanding of plant root competition and for prescribing best practise for tree establishment in agroforestry systems.     

Diversity and Specificity of Frankia Strains in Nodules of Sympatric Myrica gale, Alnus incana, and Shepherdia canadensis Determined by rrs Gene Polymorphism

The identity of Frankia strains from nodules of Myrica gale, Alnus incana subsp. rugosa, and Shepherdia canadensis was determined for a natural stand on a lake shore sand dune in Wisconsin, where the three actinorhizal plant species were growing in close proximity, and from two additional stands with M. gale as the sole actinorhizal component. Unisolated strains were compared by their 16S ribosomal DNA (rDNA) restriction patterns using a direct PCR amplification protocol on nodules. Phylogenetic relationships among nodular Frankia strains were analyzed by comparing complete 16S rDNA sequences of study and reference strains. Where the three actinorhizal species occurred together, each host species was nodulated by a different phylogenetic group of Frankia strains. M. gale strains from all three sites belonged to an Alnus-Casuarina group, closely related to Frankia alni representative strains, and were low in diversity for a host genus considered promiscuous with respect to Frankia microsymbiont genotype. Frankia strains from A. incana nodules were also within the Alnus-Casuarina cluster, distinct from Frankia strains of M. gale nodules at the mixed actinorhizal site but not from Frankia strains from two M. gale nodules at a second site in Wisconsin. Frankia strains from nodules of S. canadensis belonged to a divergent subset of a cluster of Elaeagnaceae-infective strains and exhibited a high degree of diversity. The three closely related local Frankia populations in Myrica nodules could be distinguished from one another using our approach. In addition to geographic separation and host selectivity for Frankia microsymbionts, edaphic factors such as soil moisture and organic matter content, which varied among locales, may account for differences in Frankia populations found in Myrica nodules.     

Replacement of tyrosine residues by phenylalanine in cytochrome P450cam alters the formation of Cpd II-like species in reactions with artificial oxidants

Our previous rapid-scanning stopped-flow studies of the reaction of substrate-free cytochrome P450cam with peracids [Spolitak et al. (2005) J Biol Chem 280:20300-20309; (2006) J Inorg Biochem 100:2034-2044] spectrally characterized compound I [ferryl iron plus a porphyrin pi-cation radical (Fe(IV) = O/Por(+))], as well as Cpd ES (Fe(IV) = O/Tyr.). In the present studies, we report how the substitutions in Y75F, Y96F, and Y96F/Y75F P450cam variants permit the formation of a species we attribute to Cpd II (Fe(IV) = O) in reactions with peracids and cumene hydroperoxide. These variants produce changes in hydrogen bonding patterns and increased hydrophobicity that affect the ratio of heterolytic to homolytic pathways in reactions with cumene hydroperoxide, resulting in a shift of this ratio from 84/16 for WT to 72/28 for the Y96F/Y75F double mutant. Various ways of generating the Cpd II-like species were explored, and it was possible, especially with the more hydrophobic variants, to generate large fractions of the P450cam variants as Cpd II. The Cpd II-like species is ineffective at hydroxylating camphor, but can be readily reduced by ascorbate (as well as other peroxidase substrates) to ferric P450cam, which could then bind camphor to form the high-spin heme. The difference in the spectral properties of Cpd ES and Cpd II was rationalized as possibly being due to different states of protonation.     

Markedly increased susceptibility to natural sheep scrapie of transgenic mice expressing ovine prp

The susceptibility of sheep to scrapie is known to involve, as a major determinant, the nature of the prion protein (PrP) allele, with the VRQ allele conferring the highest susceptibility to the disease. Transgenic mice expressing in their brains three different ovine PrP(VRQ)-encoding transgenes under an endogenous PrP-deficient genetic background were established. Nine transgenic (tgOv) lines were selected and challenged with two scrapie field isolates derived from VRQ-homozygous affected sheep. All inoculated mice developed neurological signs associated with a transmissible spongiform encephalopathy (TSE) disease and accumulated a protease-resistant form of PrP (PrPres) in their brains. The incubation duration appeared to be inversely related to the PrP steady-state level in the brain, irrespective of the transgene construct. The survival time for animals from the line expressing the highest level of PrP was reduced by at least 1 year compared to those of two groups of conventional mice. With one isolate, the duration of incubation was as short as 2 months, which is comparable to that observed for the rodent TSE models with the briefest survival times. No survival time reduction was observed upon subpassaging of either isolate, suggesting no need for adaptation of the agent to its new host. Overexpression of the transgene was found not to be required for transmission to be accelerated compared to that observed with wild-type mice. Conversely, transgenic mice overexpressing murine PrP were found to be less susceptible than tgOv lines expressing ovine PrP at physiological levels. These data argue that ovine PrP(VRQ) provided a better substrate for sheep prion replication than did mouse PrP. Altogether, these tgOv mice could be an improved model for experimental studies on natural sheep scrapie.     

Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

Background

While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge.

Methods

We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods.

Results

We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs).

Conclusion

Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.

     

A dynamic leaf gas‐exchange strategy is conserved in woody plants under changing ambient CO2: evidence from carbon isotope discrimination in paleo and CO2 enrichment studies

Rising atmospheric [CO₂], c_a, is expected to affect stomatal regulation of leaf gas‐exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water, and nutrient cycling of forests. Researchers have proposed various strategies for stomatal regulation of leaf gas‐exchange that include maintaining a constant leaf internal [CO₂], c_i, a constant drawdown in CO₂ (c_a ? c_i), and a constant c_i/c_a. These strategies can result in drastically different consequences for leaf gas‐exchange. The accuracy of Earth systems models depends in part on assumptions about generalizable patterns in leaf gas‐exchange responses to varying c_a. The concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these strategies, provides a unifying framework for understanding leaf gas‐exchange responses to c_a. To assess leaf gas‐exchange regulation strategies, we analyzed patterns in c_i inferred from studies reporting C stable isotope ratios (δ¹³C) or photosynthetic discrimination (?) in woody angiosperms and gymnosperms that grew across a range of c_a spanning at least 100 ppm. Our results suggest that much of the c_a‐induced changes in c_i/c_a occurred across c_a spanning 200 to 400 ppm. These patterns imply that c_a ? c_i will eventually approach a constant level at high c_a because assimilation rates will reach a maximum and stomatal conductance of each species should be constrained to some minimum level. These analyses are not consistent with canalization toward any single strategy, particularly maintaining a constant c_i. Rather, the results are consistent with the existence of a broadly conserved pattern of stomatal optimization in woody angiosperms and gymnosperms. This results in trees being profligate water users at low c_a, when additional water loss is small for each unit of C gain, and increasingly water‐conservative at high c_a, when photosystems are saturated and water loss is large for each unit C gain.     

Uptake or extrusion: crystal structures of full ABC transporters suggest a common mechanism

ATP-binding cassette (ABC) transporters are integral membrane proteins that move diverse substrates across cellular membranes. ABC importers catalyse the uptake of essential nutrients from the environment, whereas ABC exporters facilitate the extrusion of various compounds, including drugs and antibiotics, from the cytoplasm. How ABC transporters couple ATP hydrolysis to the transport reaction has long remained unclear. The recent crystal structures of four complete ABC transporters suggest that a key step of the molecular mechanism is conserved in importers and exporters. Whereas binding of ATP promotes an outward-facing conformation, the release of the hydrolysis products ADP and phosphate promotes an inward-facing conformation. This basic scheme can in principle explain ATP-driven drug export and binding protein-dependent nutrient uptake.     

Inhibition of protein phosphatase 2A activity by selective electrophile alkylation damage

Protein serine/threonine phosphatase 2A (PP2A) is a critical regulator of numerous cellular signaling processes and a potential target for reactive electrophiles that dysregulate phosphorylation-dependent signal transduction cascades. The predominant cellular form of PP2A is a heterotrimeric holoenzyme consisting of a structural A, a variable B, and a catalytic C subunit. We studied the modification of two purified PP2A holoenzyme complexes (ABalpha(FLAG)C and ABdelta(FLAG)C) with two different thiol-reactive electrophiles, biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (PEO-IAB) and the biotinamido-4-[4'-(maleimidomethyl)cyclohexanecarboxamido]butane (BMCC). In vivo treatment of HEK 293 cells with these electrophiles resulted in alkylation of all three PP2A subunits. Electrophile treatment of the immunopurified FLAG-tagged holoenzymes produced a concentration-dependent adduction of PP2A subunits, as observed by Western blot analysis. Although both electrophiles labeled all three PP2A subunits, only BMCC inhibited the catalytic activity of both holoenzymes. Alkylation patterns in the A and B subunits were identical for the two electrophiles, but BMCC alkylated four Cys residues in the C subunit that were not labeled by PEO-IAB. Homology between the catalytic subunits of PP1 and PP2A enabled generation of a comparative model structure for the C subunit of PP2A. The model structure provided additional insight into contributions of specific BMCC-Cys adducts to PP2A enzyme inhibition. The results indicate that site selectivity of protein adduction should be a critical determinant of the ability of electrophiles to affect cellular signaling processes.