Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes

Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and diversity of tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT50) was approximately 12 days in soil sampled from <30 cm depth, and increased progressively with soil depth, reaching over 84 days at 70–80 cm. In sub-soil there was a lag period of between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in top-soil samples prior to the onset of degradation. The maximum degradation rate was the same in top-soil and sub-soil samples. Although diverse tfdAα and tfdA genes were present prior to mecoprop-p degradation, real time PCR revealed that degradation was associated with proliferation of tfdA genes. The number of tfdA genes and the most probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p addition were below the limit of quantification and detection respectively. Melting curves from the real time PCR analysis showed that prior to mecoprop-p degradation both class I and class III tfdA genes were present in top- and sub-soil samples. However at all soil depths only tfdA class III genes proliferated during degradation. Denaturing gradient gel electrophoresis confirmed that class III tfdA genes were associated with mecoprop-p degradation. Degradation was not associated with the induction of novel tfdA genes in top- or sub-soil samples, and there were no apparent differences in tfdA gene diversity with soil depth prior to or following degradation.

Trends in aerosol optical depth in the Russian Arctic and their links with synoptic climatology

Temporal and spatial variability of aerosol optical depth (AOD) are examined using observations of direct solar radiation in the Eurasian Arctic for 1940-1990. AOD is estimated using empirical methods for 14 stations located between 66.2 degrees N and 80.6 degrees N, from the Kara Sea to the Chukchi Sea. While AOD exhibits a well-known springtime maximum and summertime minimum at all stations, atmospheric turbidity is higher in spring in the western (Kara-Laptev) part of the Eurasian Arctic. Between June and August, the eastern (East Siberian-Chukchi) sector experiences higher transparency than the western part. A statistically significant positive trend in AOD was observed in the Kara-Laptev sector between the late 1950s and the early 1930s predominantly in spring when pollution-derived aerosol dominates the Arctic atmosphere but not in the eastern sector. Although all stations are remote, those with positive trends are located closer to the anthropogenic sources of air pollution. By contrast, a widespread decline in AOD was observed between 1982 and 1990 in the eastern Arctic in spring but was limited to two sites in the western Arctic. These results suggest that the post-1982 decline in anthropogenic emissions in Europe and the former Soviet Union has had a limited effect on aerosol load in the Arctic. The post-1982 negative trends in AOD in summer, when marine aerosol is present in the atmosphere, were more common in the west. The relationships between AOD and atmospheric circulation are examined using a synoptic climatology approach. In spring, AOD depends primarily on the strength and direction of air flow. Thus strong westerly and northerly flows result in low AOD values in the East Siberian-Chukchi sector. By contrast, strong southerly flow associated with the passage of depressions results in high A OD in the Kara-Laptev sector and trajectory analysis points to the contribution of industrial regions of the sub-Arctic. In summer, low pressure gradient or anticyclonic conditions result in high atmospheric turbidity. The frequency of this weather type has declined significantly since the early 1980s in the Kara-Laptev sector, which partly explains the decline in summer AOD values. (c) 2004 Elsevier B.V. All rights reserved.

Depth by The Rule

This note corrects a previous treatment of algorithms for the metric DTR, Depth by the Rule.

Observations of the depth of ice particle evaporation beneath frontal cloud to improve NWP modelling

The evaporation (sublimation) of ice particles beneath frontal ice cloud can provide a significant source of diabatic cooling which can lead to enhanced slantwise descent below the frontal surface. The strength and vertical extent of the cooling play a role in determining the dynamic response of the atmosphere, and an adequate representation is required in numerical weather-prediction (NWP) models for accurate forecasts of frontal dynamics. In this paper, data from a vertically pointing 94 GHz radar are used to determine the characteristic depth-scale of ice particle sublimation beneath frontal ice cloud. A statistical comparison is made with equivalent data extracted from the NWP mesoscale model operational at the Met Office, defining the evaporation depth-scale as the distance for the ice water content to fall to 10% of its peak value in the cloud. The results show that the depth of the ice evaporation zone derived from observations is less than 1 km for 90% of the time. The model significantly overestimates the sublimation depth-scales by a factor of between two and three, and underestimates the local ice water content by a factor of between two and four. Consequently the results suggest the model significantly underestimates the strength of the evaporative cooling, with implications for the prediction of frontal dynamics. A number of reasons for the model discrepancy are suggested. A comparison with radiosonde relative humidity data suggests part of the overestimation in evaporation depth may be due to a high RH bias in the dry slot beneath the frontal cloud, but other possible reasons include poor vertical resolution and deficiencies in the evaporation rate or ice particle fall-speed parametrizations.

A comparison of the variability of biological nutrients against depth and potential density.

The main biogeochemical nutrient distributions, along with ambient ocean temperature and the light field, control ocean biological productivity. Observations of nutrients are much sparser than physical observations of temperature and salinity, yet it is critical to validate biogeochemical models against these sparse observations if we are to successfully model biological variability and trends. Here we use data from the Bermuda Atlantic Time-series Study and the World Ocean Database 2005 to demonstrate quantitatively that over the entire globe a significant fraction of the temporal variability of phosphate, silicate and nitrate within the oceans is correlated with water density. The temporal variability of these nutrients as a function of depth is almost always greater than as a function of potential density, with he largest reductions in variability found within the main pycnocline. The greater nutrient variability as a function of depth occurs when dynamical processes vertically displace nutrient and density fields together on shorter timescales than biological adjustments. These results show that dynamical processes can have a significant impact on the instantaneous nutrient distributions. These processes must therefore be considered when modeling biogeochemical systems, when comparing such models with observations, or when assimilating data into such models.

The role of flower inclination, depth, and height in the preferences of a pollinating beetle (Coleoptera : Glaphyridae)

Amphicoma ( Glaphyridae) beetles are important pollinators of red bowl-shaped flowers in the Mediterranean. The role of color and shape in flower choice is well studied but the roles of inclination, depth, and height have seldom been investigated. Under field conditions, models were used to experimentally manipulate these three characters and visitation rates of beetles were recorded. Models with red horizontal surfaces were visited significantly more often than models with red vertical surfaces. Shallow flower models were visited significantly more than deeper equivalents. Models below or at the height of natural flower populations elicited significantly more landings than models above the height of flowers. Inclination, depth, and height characteristics are all likely to be important components in the flower preferences exhibited by pollinating beetles.

Phylogenetic mixture models can reduce node-density artifacts

We investigate the performance of phylogenetic mixture models in reducing a well-known and pervasive artifact of phylogenetic inference known as the node-density effect, comparing them to partitioned analyses of the same data. The node-density effect refers to the tendency for the amount of evolutionary change in longer branches of phylogenies to be underestimated compared to that in regions of the tree where there are more nodes and thus branches are typically shorter. Mixture models allow more than one model of sequence evolution to describe the sites in an alignment without prior knowledge of the evolutionary processes that characterize the data or how they correspond to different sites. If multiple evolutionary patterns are common in sequence evolution, mixture models may be capable of reducing node-density effects by characterizing the evolutionary processes more accurately. In gene-sequence alignments simulated to have heterogeneous patterns of evolution, we find that mixture models can reduce node-density effects to negligible levels or remove them altogether, performing as well as partitioned analyses based on the known simulated patterns. The mixture models achieve this without knowledge of the patterns that generated the data and even in some cases without specifying the full or true model of sequence evolution known to underlie the data. The latter result is especially important in real applications, as the true model of evolution is seldom known. We find the same patterns of results for two real data sets with evidence of complex patterns of sequence evolution: mixture models substantially reduced node-density effects and returned better likelihoods compared to partitioning models specifically fitted to these data. We suggest that the presence of more than one pattern of evolution in the data is a common source of error in phylogenetic inference and that mixture models can often detect these patterns even without prior knowledge of their presence in the data. Routine use of mixture models alongside other approaches to phylogenetic inference may often reveal hidden or unexpected patterns of sequence evolution and can improve phylogenetic inference.

Bone morphogenetic protein-6 enhances gonadotrophin-dependent progesterone and inhibin secretion and expression of rnRNA transcripts encoding gonadotrophin receptors and inhibin/activin subunits in chicken granulosa cells

The aims were to examine ovarian expression of bone morphogenetic protein (BMP) ligands/receptor mRNAs in the chicken and to test the hypothesis that theca-derived BMP(s) modulates granulosa cell function in a paracrine manner. RT-PCR revealed expression of multiple BMPs in granulosa and theca cells from prehierarchical and preovulatory follicles with greater expression in theca cells; both cell types expressed BMP receptors-1A, -1B and -II consistent with tissue responsiveness. Preovulatory granulosa cells F1, F2 and F3/4) were cultured with BMP-6 (expressed by theca but not granulosa) in the presence/absence of LH, FSH or 8-Br-cAMP. RMP-6 increased 'basal' and gonadotrophin-induced inhibin-A and progesterone secretion by each cell type but did not enhance the effect of 8-Br-cAMP. This indicates that the observed synergism between BMP-6 and gonadotrophin might involve BMP-induced up-regulation of gonadotrophin receptors. In support of this, BMP-6 alone increased LH-receptor (LHR) mRNA in F1 cells and FSH-receptor (FSHR) mRNA in F1, F2 and F3/4 cells. RMP-6 also enhanced LH/FSH-induced LHR transcript amount in each cell type but did not raise FSHR transcript amounts above those induced by BMP-6 alone. To further explore BMP6 action on inhibin-A secretion, we quantified inhibin/activin subunits (alpha, beta(A), beta(B)) mRNAs. Consistent with its effect on inhibin-A secretion, BMP-6 enhanced 'basal' expression of alpha- and beta(A)-Subunit mRNA in F1, F2 and F3/4 cells, and beta(B)-subunit mRNA in F3/4 cells. BMP-6 markedly enhanced FSH/LH-induced expression of alpha-subunit in all follicles and FSH-induced beta(A)-subunit in F2 and F3/4 follicles but not in F1 follicles. Neither BMP-6 alone, nor FSH/LH alone, affected 'basal' OB mRNA abundance. However, co-treatment with gonadotrophin and BMP-6 greatly increased beta(B)-subunit expression, the response being lowest in F1 follicles and greatest in F3/4 follicles. Collectively, these results support the hypothesis that intra-ovarian OMPs of thecal origin have a paracrine role in modulating granulosa cell function in the chicken in a preovulatory stage-dependent manner.

Differential expression of mRNAs encoding co-receptor (betaglycan) and activin type-I preovulatory and prehierarchical follicles of the putative inhibin and type-II receptors in the laying hen ovary

Ovarian follicle development is primarily regulated by an interplay between the pituitary gonadotrophins, LH and FSH, and ovary-derived steroids. Increasing evidence implicates regulatory roles of transforming growth factor-beta (TGF beta) superfamily members, including inhibins and activins. The aim of this study was to identify the expression of mRNAs encoding key receptors of the inhibin/activin system in ovarian follicles ranging from 4 mm in diameter to the dominant F1 follicle (similar to 40 turn). Ovaries were collected (n=16) from inid-sequence hens maintained on a long-day photoschedule (16h of light:8 h of darkness). All follicles removed were dissected into individual granulosa and thecal layers. RNA was extracted and cDNA synthesized. Real-time quantitative PCR was used to quantify the expression of niRNA encoding betaglycan, activin receptor (ActR) subtypes (type-I, -IIA and -IIB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH); receptor expression data were normalized to GAPDH expression. Detectable levels of ActRI, -IIA and -IIB and the inhibin co-receptor (betaglycan) expression were found in all granulosa and thecal layers analysed. Granulosa ActRI mRNA peaked (P < 0(.)05) in 8-9(.)9 mm follicles, whereas ActRIIA rose significantly from 6-7(.)9 mm to 8-9(.)9 nun, before filling to F3/2; levels then rose sharply (3-fold) to F1 levels. Granulosa betaglycan niRNA expression rose 3-fold from 4-5(.)9 min to 8-9(.)9 mm, before falling 4-fold to F3/2; levels then rose sharply (4-fold) to F1 levels. ActRIIB levels did not vary significantly during follicular development. Thecal ActRI mRNA expression was similar from 4-7(.)9 mm then decreased significantly to a nadir at the F4 position, before increasing 2-fold to the F1 (P < 0(.)05). Although thecal ActRIIB and -IIA expression did not vary significantly from 4 nim to F3, ActRIIB expression increased significantly (2-fold) from F3 to F1 and ActIIA, increased 22-fold from F2 to F1 (P < 0(.)05). Thecal betaglycan fell to a nadir at F6 after follicle selection; levels then increased significantly to F2, before filling similar to 50% in the F I. In all follicles studied expression of betaglycan and ActRI (granulosa: 1-0(.)65, P < 0-001, n=144/group; theca: r=0(.)49, P < 0-001, n=144/group) was well correlated. No significant correlations were identified between betaglycan and ActRIIA or -IIB. Considering all follicles analysed, granulosa mRNA expression of betaglycan, ActRI ActRIIA and ActRIIB were all significantly lower than in corresponding thecal tissue (betaglycan, 11(.)4-fold; ActRIIB, 5(.)1-fold; ActR(.) 3-8-fold: ActRIIA, 2(.)8-fold). The co-localization of type-I and -II activin receptors and betaglycan on granulosa and thecal cells are consistent with a local auto/paracrine role of inhibins and activins in modulating ovarian follicle development, selection and progression in the domestic fowl.

Detecting the node-density artifact in phylogeny reconstruction

The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas of the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) to detect this artifact, and here we report the results of computer simulations that examine the test's performance. In a sample of 50,000 random data sets, we find that the delta test detects the artifact in 94.4% of cases in which it is present. When the artifact is not present (n = 10,000 simulated data sets) the test showed a type I error rate of approximately 1.69%, incorrectly reporting the artifact in 169 data sets. Three measures of tree shape or "balance" failed to predict the size of the node-density effect. This may reflect the relative homogeneity of our randomly generated topologies, but emphasizes that nearly any topology can suffer from the artifact, the effect not being confined only to highly unevenly sampled or otherwise imbalanced trees. The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating. [Delta test; molecular clock; molecular evolution; node-density effect; phylogenetic reconstruction; speciation; simulation.]