The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments

The partition matrix is a graphical tool for comparative analysis of nucleotide sequences following alignment. It is particularly useful for investigating the divergent phylogenies of sequence regions undergoing reticulate evolution. A partition matrix is generated by determining the consistency of the parsimoniously informative sites in a set of aligned sequences with the binary partitions inferred from the sequences. Since the linear order of sites is maintained, the matrix can be used to assess whether the distribution of sites either supporting or conflicting with particular partitions changes along the length of the alignment. The usefulness of the matrix in allowing visual identification of differences in evolutionary history among regions depends on the order in which partitions are shown; several suitable ordering schemes are proposed. We demonstrate the use of the partition matrix in interpreting the evolution of the pseudoautosomal boundary region on the sex chromosome of catarrhine primates. Its routine use should help to avoid attempts to derive single phylogenies from sequences whose evolution has been reticulate and to identify the gene conversion or recombination events underlying the reticulation. The method is relatively fast. It is exploratory, and it can form the basis for more formal analysis, which we discuss.      

Fertilizer nitrogen budgets of two doses of Na15NO3 dressings split-applied to winter wheat in microplots on a loam soil

In a field experiment performed in microplots, winter wheat was fertilized at two different total N dressings (135 and 180 kg ha^–1) split-applied as Na¹⁵NO₃ in three equal applications at tillering, stem elongation, and flag leaf.No significant differences were found in the percentage recovery values for the entire plant at the three split applications between the two N dressings. The total percentage recovery of fertilizer N by the plant was high and practically equal at both fertilization levels (76.65% and 75.84% for 135 and 180 kg N ha^–1, respectively); crop yields were also similar. In contrast, gaseous losses calculated after drawing up the balance sheet were, in absolute values, higher for the tillering and stem elongation split applications when using the 180 kg N ha^–1 dressing (7.67 and 4.84 kg N ha^–1, respectively) than for the 135 kg N ha^–1 dressing (3.45 and 1.26 kg N ha^–1, respectively). They were found to be zero at flag leaf at both fertilization levels. The amount of applied fertilizer N did not influence the amount of N taken up from the soil which was about 143 kg ha^–1.     

Assessment of macroenergetic parameters for an anaerobic upflow biomass bed and filter (UBF) reactor

This article reports the steady-state performance of two hybrid anaerobic digesters treating soluble synthetic sugar wastes of 1 and 0.5% strength and the assessment of the associated macroenergetic parameters (growth yield, so-called maintenance coefficient). A theoretical development shows a "nongrowth" parameter concept to be more appropriate than maintenance or decay. Combined energy and mass balances are used to develop a model for growth rate which compares well with experimental data. The COD removal efficiency had no significant effect on growth yield and the maintenance parameter, although a dual combined balance indicated the possibility of such an effect. Macroenergetic parameters did not vary significantly with the specific feeding rate of the system. We thus conclude that a single model may be used over a broad range of feeding and performance conditions.     

Genomic analysis of carbon monoxide utilization and butanol production by Clostridium carboxidivorans strain P7

Increasing demand for the production of renewable fuels has recently generated a particular interest in microbial production of butanol. Anaerobic bacteria, such as Clostridium spp., can naturally convert carbohydrates into a variety of primary products, including alcohols like butanol. The genetics of microorganisms like Clostridium acetobutylicum have been well studied and their solvent-producing metabolic pathways characterized. In contrast, less is known about the genetics of Clostridium spp. capable of converting syngas or its individual components into solvents. In this study, the type of strain of a new solventogenic Clostridium species, C. carboxidivorans, was genetically characterized by genome sequencing. C. carboxidivorans strain P7(T) possessed a complete Wood-Ljungdahl pathway gene cluster, involving CO and CO(2) fixation and conversion to acetyl-CoA. Moreover, with the exception of an acetone production pathway, all the genetic determinants of canonical ABE metabolic pathways for acetate, butyrate, ethanol and butanol production were present in the P7(T) chromosome. The functionality of these pathways was also confirmed by growth of P7(T) on CO and production of CO(2) as well as volatile fatty acids (acetate and butyrate) and solvents (ethanol and butanol). P7(T) was also found to harbour a 19 Kbp plasmid, which did not include essential or butanol production related genes. This study has generated in depth knowledge of the P7(T) genome, which will be helpful in developing metabolic engineering strategies to improve C. carboxidivorans's natural capacity to produce potential biofuels from syngas.     

Origin of p-cresol in the anaerobic degradation of trinitrotoluene

p-Cresol was repeatedly detected as a trace metabolite in anaerobic slurry reactors treating 2,4,6-trinitrotoluene (TNT)-contaminated soils. This study shows that p-cresol was not a metabolite of the anaerobic degradation of TNT, by using a combination of analytical techniques and 13C-labelled TNT. Instead, p-cresol, an intermediate in the degradation pathway of some amino acids, was shown to be inhibited by TNT and its metabolites. The range and persistence of inhibition to p-cresol microbial degradation decreased with the level of amino-substitution of the derivatives. This explains why p-cresol accumulated within the TNT-treating anaerobic bioslurry, as it could not be further biodegraded in the presence of TNT.     

Influence of the starting microbial nucleus type on the anaerobic granulation dynamics

 The influence of four different granulation precursors, syntroph-enriched methanogenic consortia, Methanosaeta-enriched, Methanosarcina-enriched nuclei and acidogenic flocs, on the time course of complex granule development and the lag time for start-up was investigated in four upflow anaerobic sludge-bed and filter reactors. Although the operational conditions allowed the maintenance of the same specific growth rate of biomass in the four reactors, granulation proceeded rapidly with syntroph/methanogenic consortia, Methanosaeta and Methanosarcina nuclei. However, granulation was significantly retarded when acidogenic flocs were used as precursors. The granule mean Sauter diameter increased rapidly in the reactor inoculated with syntroph/methanogenic consortia, Methanosaeta and Methanosarcina nuclei and reached, at the end of the experiment, 3.1, 2.7 and 2.4 mm compared to 1.1 mm in that inoculated with acidogenic flocs. This corresponded to a rate of granule size increase of 31, 21, 18 μm/day in syntroph/methanogenic consortia, Methanosaeta and Methanosarcina nuclei, respectively, compared to 7 μm/day in acidogenic flocs. Biomass specific activities (i.e. acidogenic, syntrophic and methanogenic activities) increased stepwise in all reactors with time, especially in those inoculated with syntroph/methanogenic consortia and Methanosaeta nuclei. From these results it appears that syntrophs and Methanosaeta spp. play an important role in the anaerobic granulation process. Received: 25 January 1996 / Received revision: 3 September 1996 / Accepted: 13 September 1996     

Unambiguous Detection of Multiple TP53 Gene Mutations in AAN-Associated Urothelial Cancer in Belgium Using Laser Capture Microdissection

In the Balkan and Taiwan, the relationship between exposure to aristolochic acid and risk of urothelial neoplasms was inferred from the A>T genetic hallmark in TP53 gene from malignant cells. This study aimed to characterize the TP53 mutational spectrum in urothelial cancers consecutive to Aristolochic Acid Nephropathy in Belgium. Serial frozen tumor sections from female patients (n = 5) exposed to aristolochic acid during weight-loss regimen were alternatively used either for p53 immunostaining or laser microdissection. Tissue areas with at least 60% p53-positive nuclei were selected for microdissecting sections according to p53-positive matching areas. All areas appeared to be carcinoma in situ. After DNA extraction, mutations in the TP53 hot spot region (exons 5–8) were identified using nested-PCR and sequencing. False-negative controls consisted in microdissecting fresh-frozen tumor tissues both from a patient with a Li-Fraumeni syndrome who carried a p53 constitutional mutation, and from KRas mutated adenocarcinomas. To rule out false-positive results potentially generated by microdissection and nested-PCR, a phenacetin-associated urothelial carcinoma and normal fresh ureteral tissues (n = 4) were processed with high laser power. No unexpected results being identified, molecular analysis was pursued on malignant tissues, showing at least one mutation in all (six different mutations in two) patients, with 13/16 exonic (nonsense, 2; missense, 11) and 3/16 intronic (one splice site) mutations. They were distributed as transitions (n = 7) or transversions (n = 9), with an equal prevalence of A>T and G>T (3/16 each). While current results are in line with A>T prevalence previously reported in Balkan and Taiwan studies, they also demonstrate that multiple mutations in the TP53 hot spot region and a high frequency of G>T transversion appear as a complementary signature reflecting the toxicity of a cumulative dose of aristolochic acid ingested over a short period of time.     

Risky future for Mediterranean forests unless they undergo extreme carbon fertilization

Forest performance is challenged by climate change but higher atmospheric [CO₂] (c_a) could help trees mitigate the negative effect of enhanced water stress. Forest projections using data assimilation with mechanistic models are a valuable tool to assess forest performance. Firstly, we used dendrochronological data from 12 Mediterranean tree species (six conifers and six broadleaves) to calibrate a process‐based vegetation model at 77 sites. Secondly, we conducted simulations of gross primary production (GPP) and radial growth using an ensemble of climate projections for the period 2010–2100 for the high‐emission RCP8.5 and low‐emission RCP2.6 scenarios. GPP and growth projections were simulated using climatic data from the two RCPs combined with (i) expected c_a; (ii) constant c_a = 390 ppm, to test a purely climate‐driven performance excluding compensation from carbon fertilization. The model accurately mimicked the growth trends since the 1950s when, despite increasing c_a, enhanced evaporative demands precluded a global net positive effect on growth. Modeled annual growth and GPP showed similar long‐term trends. Under RCP2.6 (i.e., temperatures below +2 °C with respect to preindustrial values), the forests showed resistance to future climate (as expressed by non‐negative trends in growth and GPP) except for some coniferous sites. Using exponentially growing c_a and climate as from RCP8.5, carbon fertilization overrode the negative effect of the highly constraining climatic conditions under that scenario. This effect was particularly evident above 500 ppm (which is already over +2 °C), which seems unrealistic and likely reflects model miss‐performance at high c_a above the calibration range. Thus, forest projections under RCP8.5 preventing carbon fertilization displayed very negative forest performance at the regional scale. This suggests that most of western Mediterranean forests would successfully acclimate to the coldest climate change scenario but be vulnerable to a climate warmer than +2 °C unless the trees developed an exaggerated fertilization response to [CO₂].