Heritabilities and quantitative trait loci for blood gases and blood pH in swine

Maintaining pH and blood gases in a narrow range is essential to sustain normal biochemical reactions. Decreased oxygenation, poor tissue perfusion, disturbance to CO₂ expiration, and shortage of HCO₃⁻ can lead to metabolic acidosis. This is a common situation in swine, and originates from a broad range of medical conditions. pH and blood gases appear to be under genetic control, and populations with physiological traits closer to the pathological thresholds may be more susceptible to developing pathological conditions. However, little is known about the genetic basis of such traits. We have therefore estimated phenotypic and genetic variability and identified quantitative trait loci (QTL) for pH and blood gases in blood samples from 139 F₂ pigs from the Meishan/Pietrain family. Samples were taken before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. Twenty-seven QTL influencing pH and blood gases were identified on nine chromosomes. Five of the QTL were significant on a genome-wide level; 22 QTL were significant on a chromosome-wide level. QTL for pH-associated traits have been mapped to SSC3, 18 and X. QTL associated with CO₂ have been detected on SSC6, 7, 8 and 9, and QTL associated with O₂ on SSC2 and SSC8. QTL showed specific health/disease patterns that were related to the physiological state of the pigs from day 0, to acute disease (day 14), convalescence (day 28) and chronic disease (day 42). The results demonstrate that pH and blood gases are influenced by multiple chromosomal areas, each with relatively small effects.     

Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon

The availability of sequence information for many plants has opened the way to advanced genetic analysis in many non-model plants. Nevertheless, exploration of genetic variation on a large scale and its use as a tool for the identification of traits of interest are still rare. In this study, we combined a bulk segregation approach with our own-designed microarrays to map the pH locus that influences fruit pH in melon. Using these technologies, we identified a set of markers that are genetically linked to the pH trait. Further analysis using a set of melon cultivars demonstrated that some of these markers are tightly linked to the pH trait throughout our germplasm collection. These results validate the utility of combining microarray technology with a bulk segregation approach in mapping traits of interest in non-model plants.     

The impact of regional landscape context on local maladaptive trait divergence: a field test using freshwater copepod acid tolerance

Theoretical work has shown that spatial landscape context can contribute to reducing local adaptation in populations depending on the spatial pattern of environmental heterogeneity, the spatial scale of distances between habitats on landscapes, and the level of habitat connectivity. However, only a handful of empirical studies have addressed the impact of regional landscape context on local trait divergence in natural populations. We tested if local adaptation in abiotic tolerance is diminished in landscapes with strong spatial heterogeneity and habitat proximity. We used a freshwater copepod (Leptodiaptomus minutus) that is known to show local adaptive divergence in acid tolerance as a study system to understand the effects of regional landscape-level spatial heterogeneity in lake/pond pH on local trait divergence. We compared local divergence in copepod acid tolerance from three types of landscapes: (i) a homogeneous pH landscape of exclusively circumneutral lakes (pH ≥ 6.0); (ii) a heterogeneous pH landscape with a mixture of acidic and circumneutral lakes; and (iii) a heterogeneous pH landscape in which relatively infrequent circumneutral ponds are embedded in a predominantly acidic landscape. We found that local adaptation to circumneutral lake/pond pH was most reduced in the pH-heterogeneous landscape dominated by acidic habitats, likely because of gene flow from surrounding nearby acidic ponds. Our study empirically confirms theoretical predictions that spatial landscape context is important for explaining regional differences in population environmental tolerances. These effects may become important for understanding regional differences in population fitness trade-offs when presented in combination with multiple stressors.     

Characterization of UMP synthase in dairy cattle heterozygous for a lethal recessive trait

UMP synthase was characterized biochemically in dairy cattle heterozygous for a deficiency of this enzyme. Both activities comprising this bifunctional enzyme are decreased, with OMP decarboxylase more affected than orotate phosphoribosyltransferase. Immunotitration of UMP synthase activity revealed the presence of the protein product of the mutant allele in the heterozygous animals. UMP synthases from normal and deficient cattle were not distinguished from one another by kinetic constants, responses to inhibitors, pH profiles, or thermal lability. It was concluded that the 50% reduction in enzyme activity in heterozygous cattle is the result of the presence of only half the normal level of catalytically active UMP synthase.     

Genetic variability at neutral markers,quantitative trait land trait in a subdivided population under selection

Genetic variability in a subdivided population under stabilizing and diversifying selection was investigated at three levels: neutral markers, QTL coding for a trait, and the trait itself. A quantitative model with additive effects was used to link genotypes to phenotypes. No physical linkage was introduced. Using an analytical approach, we compared the diversity within deme (H(S)) and the differentiation (F(ST)) at the QTL with the genetic variance within deme (V(W)) and the differentiation (Q(ST)) for the trait. The difference between F(ST) and Q(ST) was shown to depend on the relative amounts of covariance between QTL within and between demes. Simulations were used to study the effect of selection intensity, variance of optima among demes, and migration rate for an allogamous and predominantly selfing species. Contrasting dynamics of the genetic variability at markers, QTL, and trait were observed as a function of the level of gene flow and diversifying selection. The highest discrepancy among the three levels occurred under highly diversifying selection and high gene flow. Furthermore, diversifying selection might cause substantial heterogeneity among QTL, only a few of them showing allelic differentiation, while the others behave as neutral markers.     

Intraspecific trait variability shapes leaf trait response to altered fire regimes

Background and AimsUnderstanding impacts of altered disturbance regimes on community structure and function is a key goal for community ecology. Functional traits link species composition to ecosystem functioning. Changes in the distribution of functional traits at community scales in response to disturbance can be driven not only by shifts in species composition, but also by shifts in intraspecific trait values. Understanding the relative importance of these two processes has important implications for predicting community responses to altered disturbance regimes.MethodsWe experimentally manipulated fire return intervals in replicated blocks of a fire-adapted, longleaf pine (Pinus palustris) ecosystem in North Carolina, USA and measured specific leaf area (SLA), leaf dry matter content (LDMC) and compositional responses along a lowland to upland gradient over a 4 year period. Plots were burned between zero and four times. Using a trait-based approach, we simulate hypothetical scenarios which allow species presence, abundance or trait values to vary over time and compare these with observed traits to understand the relative contributions of each of these three processes to observed trait patterns at the study site. We addressed the following questions. (1) How do changes in the fire regime affect community composition, structure and community-level trait responses? (2) Are these effects consistent across a gradient of fire intensity? (3) What are the relative contributions of species turnover, changes in abundance and changes in intraspecific trait values to observed changes in community-weighted mean (CWM) traits in response to altered fire regime?Key ResultsWe found strong evidence that altered fire return interval impacted understorey plant communities. The number of fires a plot experienced significantly affected the magnitude of its compositional change and shifted the ecotone boundary separating shrub-dominated lowland areas from grass-dominated upland areas, with suppression sites (0 burns) experiencing an upland shift and annual burn sites a lowland shift. We found significant effects of burn regimes on the CWM of SLA, and that observed shifts in both SLA and LDMC were driven primarily by intraspecific changes in trait values.ConclusionsIn a fire-adapted ecosystem, increased fire frequency altered community composition and structure of the ecosystem through changes in the position of the shrub line. We also found that plant traits responded directionally to increased fire frequency, with SLA decreasing in response to fire frequency across the environmental gradient. For both SLA and LDMC, nearly all of the observed changes in CWM traits were driven by intraspecific variation.     

Detection of quantitative trait loci for meat quality traits in cattle

A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais × Holstein experimental population. Loin muscle samples were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem. A sensory assessment was performed on grilled loin and roasted silverside joints by trained panellists. A linear regression analysis based on 165 markers revealed 35 QTL at the 5% chromosome-wide significance level (20 for sensory traits and 15 for physical and chemical traits), five of which were highly significant ( F -value: ≥9). The most significant QTL was located on chromosome 6 (with the best likely position at 39 cM) and affected haem pigment concentration. The Holstein allele for this QTL was associated with an increase of 0.53 SD in the haem scores. A QTL for pH_24h was identified on chromosome 14 (at 40 cM) and a QTL for moisture content was identified on chromosome 22 (at 21 cM). Two highly significant QTL were identified for sensory panel-assessed traits: beef odour intensity (grilled sample) on chromosome 10 (at 119 cM), and juiciness (roast sample) on chromosome 16 (at 70 cM). The proportion of phenotypic variance explained by the significant QTL ranged from 3.6% (for nitrogen content on chromosome 10) to 9.5% (for juiciness, roast sample on chromosome 16).     

The Intracellular pH of Clostridium paradoxum, an Anaerobic, Alkaliphilic, and Thermophilic Bacterium

When the extracellular pH was increased from 7.6 to 9.8, Clostridium paradoxum, a novel alkalithermophile, increased its pH gradient across the cell membrane ((Delta)pH, pH(infin) - pH(infout)) by as much as 1.3 U. At higher pH values (>10.0), the (Delta)pH and membrane potential ((Delta)(psi)) eventually declined, and the intracellular pH increased significantly. Growth ceased when the extracellular pH was greater than 10.2 and the intracellular pH increased to above 9.8. The membrane potential increased to 110 (plusmn) 8.6 mV at pH 9.1, but the total proton motive force ((Delta)p) declined from about 65 mV at pH 7.6 to 25 mV at pH 9.8. Between the extracellular pH of 8.0 and 10.3, the intracellular ATP concentration was around 1 mM and decreased at lower and higher pH values concomitantly with a decrease in growth rate.     

TNAP, TrAP, ecto-purinergic signaling, and bone remodeling

Bone remodeling is a process of continuous resorption and formation/mineralization carried out by osteoclasts and osteoblasts, which, along with osteocytes, comprise the bone multicellular unit (BMU). A key component of the BMU is the bone remodeling compartment (BRC), isolated from the marrow by a canopy of osteoblast-like lining cells. Although much progress has been made regarding the cytokine-dependent and hormonal regulation of bone remodeling, less attention has been placed on the role of extracellular pH (pH(e)). Osteoclastic bone resorption occurs at acidic pH(e). Furthermore, osteoclasts can be regarded as epithelial-like cells, due to their polarized structure and ability to form a seal against bone, isolating the lacunar space. The major ecto-phosphatases of osteoclasts and osteoblasts, acid and alkaline phosphatases, both have ATPase activity with pH optima several units different from neutrality. Furthermore, osteoclasts and osteoblasts express plasma membrane purinergic P2 receptors that, upon activation by ATP, accelerate bone osteoclast resorption and impair osteoblast mineralization. We hypothesize that these ecto-phosphatases help regulate [ATP](e) and localized pH(e) at the sites of bone resorption and mineralization by pH-dependent ATP hydrolysis coupled with P2Y-dependent regulation of osteoclast and osteoblast function. Furthermore, osteoclast cellular HCO3(-), formed as a product of lacunar V-ATPase H(+) secretion, is secreted into the BRC, which could elevate BRC pH(e), in turn affecting osteoblast function. We will review the existing data addressing regulation of BRC pH(e), present a hypothesis regarding its regulation, and discuss the hypothesis in the context of the function of proteins that regulate pH(e).     

Quantitative trait locus analysis of longitudinal quantitative trait data in complex pedigrees

There is currently considerable interest in genetic analysis of quantitative traits such as blood pressure and body mass index. Despite the fact that these traits change throughout life they are commonly analyzed only at a single time point. The genetic basis of such traits can be better understood by collecting and effectively analyzing longitudinal data. Analyses of these data are complicated by the need to incorporate information from complex pedigree structures and genetic markers. We propose conducting longitudinal quantitative trait locus (QTL) analyses on such data sets by using a flexible random regression estimation technique. The relationship between genetic effects at different ages is efficiently modeled using covariance functions (CFs). Using simulated data we show that the change in genetic effects over time can be well characterized using CFs and that including parameters to model the change in effect with age can provide substantial increases in power to detect QTL compared with repeated measure or univariate techniques. The asymptotic distributions of the methods used are investigated and methods for overcoming the practical difficulties in fitting CFs are discussed. The CF-based techniques should allow efficient multivariate analyses of many data sets in human and natural population genetics.     

A whole genome scanning for quantitative trait loci on traits related to sperm quality and ejaculation in pigs

To identify quantitative trait loci (QTL) for traits related to semen and ejaculation, phenotype data including semen volume, sperm concentration, total sperm per ejaculate, sperm motility, sperm abnormality rate, semen pH value, ejaculation times and ejaculation duration were measured on 206 F(2) boar at 240 days in a White Duroc x Erhualian intercross. A genome-wide scan was performed and the entire White Duroc x Erhualian intercross was genotyped for 183 microsatellite markers covering the whole pig genome. QTL analysis was performed using a composite regression interval mapping method via QTLExpress. A total of 18 QTL were detected, including 4 genome-wide significant QTL each for semen pH on pig chromosome (SSC) 2 and SSC12, for semen volume on SSC15, and for ejaculation times on SSC17. Fourteen suggestive QTL were found on SSC1, 2, 3, 4, 6, 9, 17 and 18. To our knowledge, this is the first report about the QTL for semen and ejaculation traits in pigs, providing a start point to decipher the genetic basis of these complex traits.     

The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein

Pectate lyase C (pelC) was the first protein in which the parallel beta-helix structure was recognized. The unique features of parallel beta-helix-containing proteins-a relatively simple topology and unusual interactions among side chains-make pelC an interesting protein to study with respect to protein folding. In this paper, we report studies of the unfolding equilibrium of pelC. PelC is unfolded reversibly by gdn-HCl at pH 7 and 5, as monitored by far- and near-UV CD and fluorescence. The coincidence of these spectroscopically detected transitions is consistent with a two-state transition at pH 7, but the three probes are not coincident at pH 5. No evidence was found for a loosely folded intermediate in the transition region at pH 5. At pH 7, the for unfolding is 12.2 kcal/mol, with the midpoint of the transition at 0.99 M gdn-HCl and m = 12.3 kcal/(mol.M). Thus, pelC is unusually stable and has an m value that is much larger than for typical globular proteins. Thermal denaturation of pelC has been studied by differential scanning calorimetry (DSC) and by CD. Although thermal denaturation is not reversible, valid thermodynamic data can be obtained for the unfolding transition. DeltaH(van't Hoff)/DeltaH(cal) is less than 1 for pHs between 5 and 8, with a maximum value of 0.91 at pH 7 decreasing to 0.85 at pH 8 and to 0.68 at pH 5. At all pHs studied, the excess heat capacity can be deconvoluted into two components corresponding to two-state transitions that are nearly coincident at pH 7, but deviate more at higher and lower pH. Thus, pelC appears to consist of two domains that interact strongly and unfold in a cooperative fashion at pH 7, but the cooperativity decreases at higher and lower pH. The crystal structure of pelC shows no obvious domain structure, however.     

Culture medium pH is influenced by basal medium,carbohydrate source,gelling agent,activated charcoal,and medium storage method

Summary When four carbohydrates were tested against six commonly cited inorganic basal media, post-autoclave pH was highest for carbohydrate-free and sucrose containing media, and progressively lower for maltoseglucose and fructose-containing media, respectively. Post-autoclave pH for these media without carbohydrates was related to medium buffering capacity. Addition of gelling agents (10 of 11 tested) increased the postautoclave pH of MS medium containing sucrose. Neutralized and acid-washed activated charcoal also increased the post-autoclave pH of liquid and agarsolidified MS medium, and the pH changed further during 8 weeks of storage. Changes in medium pH caused by gelling agents, but not charcoal, could be alleviated by adjusting the pH after their addition but prior to autoclaving.     

Soil conditions and phylogenetic relatedness influence total community trait space during early plant succession

Aims The total space of traits covered by the members of plant communities is an important parameter of ecosystem functioning and complexity. We trace the variability of trait space during early plant succession and ask how trait space co-varies with phylogenetic community structure and soil conditions. Particularly, we are interested in the small-scale variability in trait space and the influence of biotic and abiotic filters.Methods We use data on species richness and soil conditions from the first 7 years of initial succession of an artificial catchment in north-eastern Germany. Total functional attribute diversity serves as a proxy to total trait space.Important findings Total trait space steadily increased during succession. We observed high small-scale variability in total trait space that was positively correlated with species richness and phylogenetic segregation and negatively correlated with total plant cover. Trait space increased with soil carbonate content, while pH and the fraction of sandy material behaved indifferently. Our results indicate that during early succession, habitat filtering processes gain importance leading to a lesser increase in trait space than expected from the increase in species richness alone.     

Relationships between extracellular pH, intracellular pH, and gene expression in Dictyostelium discoideum

A variety of studies have shown that differentiation of Dictyostelium discoideum amoebae in the presence of cAMP is strongly influenced by extracellular pH and various other treatments thought to act by modifying intracellular pH. Thus conditions expected to lower intracellular pH markedly enhance stalk cell formation, while treatments with the opposite effect favor spores. To directly test the idea that intracellular pH is a cell-type-specific messenger in Dictyostelium, we have measured intracellular pH in cells exposed to either low extracellular pH plus weak acid or high extracellular pH plus weak base using 31P nuclear magnetic resonance (NMR). Our results show that there is no significant difference in intracellular pH (cytosolic or mitochondrial) between pH conditions which strongly promote either stalk cell or spore formation, respectively. We have also examined the effects of external pH on the expression of various cell-type-specific markers, particularly mRNAs. Some mRNAs, such as those of the prestalk II (PL1 and 2H6) and prespore II (D19, 2H3) categories, are strongly regulated by external pH in a manner consistent with their cell-type specificity during normal development. Other markers such as mRNAs D14 (prestalk I), D18 (prespore I), 10C3 (common), or the enzyme UDP-galactose polysaccharide transferase are regulated only weakly or not at all by external pH. In sum, our results show that modulation of phenotype by extracellular pH in cell monolayers incubated with cAMP does not precisely mimic the regulation of stalk and spore pathways during normal development and that this phenotypic regulation by extracellular pH does not involve changes in intracellular pH.     

Floral zygomorphy, the recurring evolution of a successful trait

The flowers of the primitive angiosperm plants were radially symmetrical (actinomorphic). Flowers with bilateral symmetry (zygomorphic) evolved in several clades independently as an adaptation to specialized methods of pollination and played an important role in the diversification of flowering plants. In the model species Antirrhinum majus (snapdragon), the related genes CYCLOIDEA (CYC) and DICHOTOMA (DICH) are key in the development of this trait. This raises the question of whether they played a role in the evolution of floral bilateral symmetry. To address this, the evolution of CYC in relation to the evolution of zygomorphy is being investigated. Phylogenetic and functional analyses of CYC-like genes are being carried out in groups either closely related to Antirhinum or in families where zygomorphy evolved as an independent event. In addition, the origin of zygomorphy is being studied by comparing the function of CYC-like genes in species with zygomorphic flowers with their function in species with radially symmetrical flowers.     

Synthesis of ATP and free radicals in an aqueous solution, containing NADH, riboflavin, ADP and inorganic phosphate

pH-dependence of initial (admixture) adenosine triphosphate (ATP) changes (ATP synthesis and hydrolysis) was studied for aerated and deaerated aqueous solutions during the incubation of adenosine diphosphate (ADP) and inorganic phosphate (Pi) in the presence of reduced nicotinamide adenine dinucleotide (NADH) and riboflavin (Rf). The preferential pH regions were indicated both for ATP synthesis and ATP hydrolysis (pH less than pH 5.4, 5.9 divided by pH 6.5 and pH greater than 6.6, pH 5.5 divided by pH 5.8 respectively). 'Free radical content measurements were paralleled by ESR technique. On the basis of the obtained results it was assumed that a part of ESP signal attributed to ADP radicals was increased during ATP synthesis.     

Relationships among site characteristics,taxonomical structure and functional trait distribution of arthropods in forest,urban and agricultural soils of Southern Italy

Urbanization and agriculture cause alterations in soil biodiversity. As arthropods quickly respond to soil changes, they have been recognized as good indicators of soil quality. This study aimed to evaluate if (1) soil physico-chemical properties act as environmental filters of the functional trait distribution of soil arthropod community; (2) the abundance of certain functional traits is linked to different land uses; (3) the taxonomical and functional approaches provide complementary information about the evaluation of biological soil quality. The study was performed at forest, agricultural and urban sites in downtown and surroundings of Naples. The soils were characterized for texture, pH, organic matter content, water content, total Cd, Cr, Cu, Ni, Pb and Zn concentrations. The forest soils showed the highest organic matter and water contents, and the lowest metal concentrations; the agricultural soils showed the lowest organic matter and water contents and high Cd and Cu concentrations, whereas the urban soils showed high Pb and Zn concentrations. The forest soils showed the highest arthropod density, taxa richness and diversity. The distribution of the functional traits in the arthropod communities of the different land uses highlighted similarity only for the preference to occupy soil and for the percentage contribution of detritivores. The abundance of arthropods living above litter and omnivores were positively correlated to Pb and Zn concentrations, whereas predators were positively correlated to Cu concentrations. The findings suggest that the arthropod identification at order level could be enough to detect differences in functional traits among forest, urban, and agricultural soils.