Randomly amplified polymorphic DNA analysis of Xylella fastidiosa Pierce's disease and oak leaf scorch pathotypes.

Randomly amplified polymorphic DNA analysis was conducted with 14 primers to 17 strains of Xylella fastidiosa. There was a high degree of similarity among the seven Pierce's disease (PD) strains (Sxy > 0.93) and the seven oak leaf scorch (OLS) strains (Sxy > 0.96). However, the two groups were different, with a similarity index of 0.67, confirming the presence of a PD DNA cluster and suggesting the presence of a new OLS cluster. The control plum leaf scald strains (two strains) together with the periwinkle wilt strain had a much smaller similarity index (0.44) compared with the PD and OLS clusters.     

Variants associated with common disease are not unusually differentiated in frequency across populations

Genetic variants that contribute to risk of common disease may differ in frequency across populations more than random variants in the genome do, perhaps because they have been exposed to population-specific natural selection. To assess this hypothesis empirically, we analyzed data from two groups of single-nucleotide polymorphisms (SNPs) that have shown reproducible (n = 9) or reported (n = 39) associations with common diseases. We compared the frequency differentiation (between Europeans and Africans) of the disease-associated SNPs with that of random SNPs in the genome. These common-disease-associated SNPs are not significantly more differentiated across populations than random SNPs. Thus, for the data examined here, ethnicity will not be a good predictor of genotype at many common-disease-associated SNPs, just as it is rarely a good predictor of genotype at random SNPs in the genome.     

Hypervariations of a protease-encoding gene, PD0218 (pspB), in Xylella fastidiosa strains causing almond leaf scorch and Pierce's disease in California

Xylella fastidiosa is a gram-negative plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce's disease (PD) of grape in many regions of North America and Mexico. Of the two 16S rRNA gene genotypes described in California, A genotype strains cause ALSD only and G genotype strains cause both PD and ALSD. While G genotype strains cause two different diseases, little is known about their genetic variation. In this study, we identified a putative protease locus, PD0218 (pspB), in the genome of X. fastidiosa and evaluated the variation at this locus in X. fastidiosa populations. PD0218 contains tandem repeats of ACDCCA, translated to threonine and proline (TP), upstream of the putative protease conserved domain. Among 116 X. fastidiosa ALSD and PD strains isolated from seven locations in California, tandem repeat numbers (TRNs) varied from 9 to 47, with a total of 30 TRN genotypes, indicating that X. fastidiosa possesses an active mechanism for contracting and expanding tandem repeats at this locus. Significant TRN variation was found among PD strains (mean = 29.9), which could be further divided into two TRN groups: PD-G(small) (mean = 17.3) and PD-G(large) (mean = 44.3). Less variation was found in ALSD strains (mean = 21.7). The variation was even smaller after ALSD strains were subdivided into the A and G genotypes (mean = 13.3, for the G genotype; mean = 27.1, for the A genotype). Genetic variation at the PD0218 locus is potentially useful for sensitive discrimination of X. fastidiosa strains. However, TRN stability, variation range, and correlation to phenotypes should be evaluated in epidemiological applications such as pathotype identification and delineation of pathogen origin.     

Glycosidases and acid-invertase activities are not correlated with Phaseolus hypocotyl growth

Changes in α-galactosidase, β-galactosidase, β-glucosidase and acid invertase activities were examined in Phaseolus vulgaris hypocotyls treated with gibberellic acid (GA), naphthyl acetic acid (NAA) and distilled water (DW) (control) in light condition. The activities were estimated both in cytoplasmic and ionically wall-bound fraction. The upper segment showed considerable elongation growth while there was hardly any growth in lower segment. GA and NAA showed distinct promotion and inhibition respectively in hypocotyl growth in upper segment. The glycosidase activities were detected in both the fractions but the activity was more pronounced in cytoplasmic than in wall fraction. Acid invertase activity was present only in cytoplasmic fraction. In lower segment, in both cytoplasmic and wall fraction, the glycosidase activity, in general, showed a decreasing trend and no effect of treatment could be envisaged. In upper segment, though the trend was similar to the lower one, in α- and β-galactosidase NAA treated segment had more activity. Invertase activity also did not show a clear trend to implicate its function in hypocotyl elongation growth. The results are discussed in relation to establishing a correlation between an activity (glycosidase and invertase) and a physiological process (hypocotyl elongation). It is concluded that these wall-loosening enzymes have no role in elongation growth of Phaseolus vulgaris hypocotyls.     

Changes in sulfate-reducing bacterial populations during the onset of black band disease

Factors that facilitate the onset of black band disease (BBD) of corals remain elusive, though anoxic conditions under the complex microbial mat and production of sulfide are implicated in necrosis of underlying coral tissues. This study investigated the diversity and quantitative shifts of sulfate-reducing bacterial (SRB) populations during the onset of BBD using real-time PCR (RT-PCR) and cloning approaches targeting the dissimilatory (bi)sulfite reductase (dsrA) gene. A quantitativePCR (qPCR) assay targeting the 16S rRNA gene also provided an estimate of total bacteria, and allowed the relative percentage of SRB within the lesions to be determined. Three Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CPs) (comprising microbial communities unlike those of BBD lesions), were tagged and followed through time as CP developed into BBD. The dsrA-targeted qPCR detected few copies of the gene in the CP samples (<65 per ng DNA), though copy numbers increased in BBD lesions (>2500 per ng DNA). SRB in CP samples were less than 1% of the bacterial population, though represented up to 7.5% of the BBD population. Clone libraries also demonstrated a shift in the dominant dsrA sequences as lesions shifted from CP into BBD. Results from this study confirm that SRB increase during the onset of BBD, likely increasing sulfide concentrations at the base of the microbial mat and facilitating the pathogenesis of BBD.     

Spontaneous eyeblinks are correlated with responses during the Stroop task

The timing and frequency of spontaneous eyeblinking is thought to be influenced by ongoing internal cognitive or neurophysiological processes, but how precisely these processes influence the dynamics of eyeblinking is still unclear. This study aimed to better understand the functional role of eyeblinking during cognitive processes by investigating the temporal pattern of eyeblinks during the performance of attentional tasks. The timing of spontaneous eyeblinks was recorded from 28 healthy subjects during the performance of both visual and auditory versions of the Stroop task, and the temporal distributions of eyeblinks were estimated in relation to the timing of stimulus presentation and vocal response during the tasks. We found that the spontaneous eyeblink rate increased during Stroop task performance compared with the resting rate. Importantly, the subjects (17/28 during the visual Stroop, 20/28 during the auditory Stroop) were more likely to blink before a vocal response in both tasks (150-250 msec) and the remaining subjects were more likely to blink soon after the vocal response (200-300 msec), regardless of the stimulus type (congruent or incongruent) or task difficulty. These findings show that spontaneous eyeblinks are closely associated with responses during the performance of the Stroop task on a short time scale and suggest that spontaneous eyeblinks likely signal a shift in the internal cognitive or attentional state of the subjects.     

Transcribed microsatellite allele lengths are often correlated with gene expression in natural sunflower populations

Microsatellites are common in genomes of most eukaryotic species. Due to their high mutability, an adaptive role for microsatellites has been considered. However, little is known concerning the contribution of microsatellites towards phenotypic variation. We used populations of the common sunflower (Helianthus annuus) at two latitudes to quantify the effect of microsatellite allele length on phenotype at the level of gene expression. We conducted a common garden experiment with seed collected from sunflower populations in Kansas and Oklahoma followed by an RNA‐Seq experiment on 95 individuals. The effect of microsatellite allele length on gene expression was assessed across 3,325 microsatellites that could be consistently scored. Our study revealed 479 microsatellites at which allele length significantly correlates with gene expression (eSTRs). When irregular allele sizes not conforming to the motif length were removed, the number of eSTRs rose to 2,379. The percentage of variation in gene expression explained by eSTRs ranged from 1%–86% when controlling for population and allele‐by‐population interaction effects at the 479 eSTRs. Of these eSTRs, 70.4% are in untranslated regions (UTRs). A gene ontology (GO) analysis revealed that eSTRs are significantly enriched for GO terms associated with cis‐ and trans‐regulatory processes. Our findings suggest that a substantial number of transcribed microsatellites can influence gene expression.     

Cicadomorpha insects associated with bacterial leaf scorch infected oak in central New Jersey

Potential insect vectors for transmission of oak leaf scorch caused by Xylella fastidiosa Wells et al., in pin and red oaks in New Jersey were surveyed by placing yellow sticky card traps in tree canopies and fogging with pyrethrin insecticide during 2002-2006. Thirty-seven Cicadomorpha species were collected from 20 genera in Membracidae, Cicadellidae, Aphrophoridae, and Clastopteridae. Of the 12,880 potential vectors collected, 91.4% were Membracidae, 6.9% were Cicadellidae, and 1.7% were Aphrophoridae and Clastopteridae. Fogging collected more insect species and individuals than sticky card collections. Sticky card sampling, done more frequently and at a larger number of locations provided similar community structure information as fogging. Sticky card collections of the dominant treehopper species, Ophiderma definita Woodruff were male biased when females were gravid. O. definita populations peaked in early June, comprised 68.2% of the total collection, and were more abundant in pin oaks than red oaks. Graphocephala versuta (Say) peaked in mid-July, comprising 6.2% of the total collection. Higher Cicadomorpha populations were observed in asymptomatic oak canopies than in neighboring X. fastidiosa infected oaks. Individual insect specimens collected from oaks were subjected to a X. fastidiosa DNA assay by polymerase chain reaction amplification. The average X. fastidiosa positive rate was 13.89% for all specimens tested. Eleven treehopper species, six leafhopper species, and four spittlebug species tested DNA positive for X. fastidiosa.     

Leaf hydraulic conductivity and photosynthesis are genetically correlated in an annual grass

Comparative studies suggest that a positive correlation between xylem water transport and photosynthesis is adaptive. A requirement for the adaptive evolution of coordination between xylem and photosynthetic functions is the presence of genetic variation and covariation for these traits within populations. Here it was determined whether there was genetic variation and covariation for leaf blade hydraulic conductivity (K(W)), photosynthetic rate (A), stomatal conductance (g(s)), and time to flowering in a population of recombinant inbred lines of Avena barbata, a Mediterranean annual grass. Significant (P < 0.05) broad-sense heritabilities (H(2)) were detected for K(W) (H(2) = 0.33), A (H(2) = 0.23) and flowering time (H(2) = 0.62), but not for g(s). Significant positive genetic covariation between A and K(W) was also observed. There was no other genetic covariation among traits. The first evidence of genetic variation for K(W) within a species was obtained. These results also indicate that there is a genetic basis for the positive association between xylem water transport and photosynthesis. The presence of significant genetic variation and covariation for these traits in natural populations would facilitate correlated evolution between xylem and leaf functions.     

Bayesian models for the analysis of genetic structure when populations are correlated

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.     

Auxin dynamics after decapitation are not correlated with the initial growth of axillary buds

One of the first and most enduring roles identified for the plant hormone auxin is the mediation of apical dominance. Many reports have claimed that reduced stem indole-3-acetic acid (IAA) levels and/or reduced basipetal IAA transport directly or indirectly initiate bud growth in decapitated plants. We have tested whether auxin inhibits the initial stage of bud release, or subsequent stages, in garden pea (Pisum sativum) by providing a rigorous examination of the dynamics of auxin level, auxin transport, and axillary bud growth. We demonstrate that after decapitation, initial bud growth occurs prior to changes in IAA level or transport in surrounding stem tissue and is not prevented by an acropetal supply of exogenous auxin. We also show that auxin transport inhibitors cause a similar auxin depletion as decapitation, but do not stimulate bud growth within our experimental time-frame. These results indicate that decapitation may trigger initial bud growth via an auxin-independent mechanism. We propose that auxin operates after this initial stage, mediating apical dominance via autoregulation of buds that are already in transition toward sustained growth.     

Repeated bout effect is not correlated with intraindividual variability during muscle-damaging exercise

The aim of this study was to test the hypothesis that the repeated bout effect depends on intraindividual variability during a second bout of eccentric exercise. Eleven healthy men performed 2 resistance training bouts consisting of maximal eccentric exercise (EE1 and EE2) using the knee extensor muscles. The interval between the exercise bouts was 2 weeks and consisted of 10 sets of 12 repetitions at 160° · s(-1). Maximal isokinetic concentric torque at 30° · s(-1) was measured before the bouts and 2 minutes and 24 hours thereafter. Muscle soreness score and creatine kinase activity were determined before and after exercise. Intraindividual variability in torque during each eccentric repetition was measured during exercise. Repeated bout effect manifested after EE2: Muscle soreness was less, the shift in optimal knee joint angle to a longer muscle length was less, and the decrease in isokinetic concentric torque 2 minutes after exercise was less for EE2 compared with that for EE1. During concentric (isokinetic) contraction, length-dependent changes in isokinetic torque (IT) occurred after both EE1 and EE2: The shorter the muscle length, the greater the change in IT. There was a significant relationship between the decrease in maximal isokinetic knee extension torque 24 hours after EE1 and intraindividual variability of EE1 (R2 = 0.71, p < 0.05), but this relationship was not significant for EE2 (R2 = 0.18). It seems that intraindividual variability during eccentric exercise protects against muscle fatigue and damage during the first exercise bout but not during a repeat bout. These findings may be useful to coaches who wish to improve muscle function in resistance training with less depression in muscle function and discomfort of their athletes, specifically, when muscle is most sensitive to muscle-damaging exercise.     

Internal acidification and cAMP increase are not correlated in Saccharomyces cerevisiae

Addition of glucose to a yeast suspension can produce both an increase in the level of cAMP and a decrease in the intracellular pH. This observation led to the idea that internal acidification triggers the cAMP increase. We have tested this hypothesis using different approaches. To study the effect of sugar metabolism on internal pH we added to the yeast either glucose or a sugar, like xylose, that cannot be phosphorylated. We also utilized yeast strains lacking hexose kinases or phosphoglucose isomerase. We found that phosphorylation of the sugar added is a requisite for internal acidification but not for the cAMP increase. Internal acidification is due to an imbalance between the rate of the metabolic reactions that generate protons and the rate at which protons can be pumped out of the cell. We have manipulated the excretion of protons by using yeast harvested at different phases of growth and resuspended in a medium with or without added K+. Addition of glucose produced a marked drop in internal pH only when the yeast was harvested in the stationary phase of growth and transferred to a medium without added K+. In contrast an increase in cAMP was observed in all situations. We conclude that in yeast there is no correlation between internal acidification and cAMP increase.     

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.     

Translation efficiencies of synonymous codons are not always correlated with codon usage in tobacco chloroplasts

Codon usage in chloroplasts is different from that in prokaryotic and eukaryotic nuclear genomes. However, no experimental approach has been made to analyse the translation efficiency of individual codons in chloroplasts. We devised an in vitro assay for translation efficiencies using synthetic mRNAs, and measured the translation efficiencies of five synonymous codon groups in tobacco chloroplasts. Among four alanine codons (GCN, where N is U, C, A or G), GCU was the most efficient for translation, whereas the chloroplast genome lacks tRNA genes corresponding to GCU. Phenylalanine and tyrosine are each encoded by two codons (UUU/C and UAU/C, respectively). Phenylalanine UUC and tyrosine UAC were translated more than twice as efficiently than UUU and UAU, respectively, contrary to their codon usage, whereas translation efficiencies of synonymous codons for alanine, aspartic acid and asparagine were parallel to their codon usage. These observations indicate that translation efficiencies of individual codons are not always correlated with codon usage in vitro in chloroplasts. This raises an important issue for foreign gene expression in chloroplasts.     

Salivary hormone concentrations in mothers and fathers becoming parents are not correlated

A time- and date-matched set of saliva samples (N = 229) from nine couples first expecting, and then caring for, their first child were used to test whether hormone changes in the father could be predicted by the hormonal status of the mother. Testosterone, cortisol, and estradiol were quantified from saliva. Neither testosterone nor estradiol concentration was correlated within couples before or after the birth, although there was a positive correlation for cortisol concentration in the mother and father before the birth. As the hormone that might be influenced by chemical signals, that already played a similar role in men and women, and that had been empirically linked to paternal behavior, cortisol concentration was also compared with sex steroid concentrations. The mother's cortisol concentration was positively correlated to the father's testosterone concentration, and the mother's testosterone concentration was positively correlated with the father's cortisol concentration. However, both effects were similar in magnitude to the cortisol to cortisol correlation, and all could parsimoniously be explained by similar responses to a shared environment. Thus, this analysis rejects parallels in peripheral hormone concentrations of estradiol, testosterone, and cortisol in mothers and fathers. However, the available data were not able to test or reject hypotheses about local neuroendocrine homology, nor to control for masking effects of other hormonal demands on men and women, nor to determine the relative importance of shared environment versus mother-father signaling.     

Evolution of gene sequence and gene expression are not correlated in yeast

We show that, in yeast, the divergence rate of gene expression is not correlated with that of its associated coding sequence. Gene essentiality influences both modes of evolution, but other properties related to protein structure or promoter composition are only correlated with coding-sequence divergence or gene expression divergence, respectively. Based on these findings, we discuss the possibilities of neutral evolution of gene expression and of different modes of evolution in unicellular versus multicellular organisms.