Encapsulation of Azotobacter vinelandii ATCC 12837 in Alginate-Na Beads as a Tomato Seedling Inoculant.

Encapsulation is an immobilization method characterized by restricting microbial cells to a delimited area while preserving their metabolic viability. This technique represents an alternative to improve the adaptive capacity of bacteria in the face of interactions with native microorganisms and environmental factors that limit their inoculation. This study aimed to evaluate the effect of Azotobacter vinelandii ATCC 12837 encapsulated in alginate-Na beads as an inoculant of tomato (Solanum Lycopersicum L) seedlings. Two inoculation treatments were carried out: liquid and encapsulated, and the control without microorganisms. Physiological variables, microbial viability, and the presence of A. vinelandii were determined by qPCR. Inoculation with A. vinelandii in liquid and encapsulated form favored seedling growth. Plants with the encapsulated inoculum significantly increased germination percentage (20%), stem diameter (38%), seedling height (34%), root length (69%), NO3 concentration (41%), and Na (30%); compared to the control. Encapsulation of A. vinelandii in alginate-Na macrocapsules allowed its establishment in the rhizosphere and was corroborated by viable count and molecular methods. The viability of the bacteria was maintained for 28 days using both inoculation methods, and not detected in the control treatment.

The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila.

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects--modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the magnitude of the Faster-X effect, ruling out the possibility that it reflects less Hill-Robertson interference for X-linked genes.

Applying the Global Monitoring Plan and analysis of POPs results in atmospheric air in Mexico (2017-2018).

Air is one of the target matrices of the Global Monitoring Plan (GMP) of the Stockholm Convention to determine concentrations and transport of Persistent Organic Pollutants (POPs). Mexico participates in the GMP for POPs in ambient air through the AIR-Global Environment Facility (GEF) program. The objective of this study was to analyze the results of POPs monitoring of air samples collected in Los Mochis, Sinaloa, Mexico, between 2017 and 2018. Passive samplers were used for the determination of chlorinated basic POPs, indicator polychlorinated biphenyls (Ind. PCBs), polybrominated biphenyl ethers (PBDEs), polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (dl-PCBs). A principal component analysis was applied to determine relationships between pollutants and groups present in the ambient air of the rural study area. Of the total POPs analyzed, 85.56% were detected in ambient air samples from Mexico. Organochlorine compounds, as DDT derivatives, were identified mainly, as well as PBDEs, PCDDs, and PCDFs. The prevalence of compounds differed according to the seasonality of sampling, with no change in average concentration between monitoring years.

Growth, respiratory activity and chlorpyrifos biodegradation in cultures of Azotobacter vinelandii ATCC 12837.

This study aimed to evaluate the growth, respiratory activity, and biodegradation of chlorpyrifos in cultures of Azotobacter vinelandii ATCC 12837. A strategy based on the modification of culture media and aeration conditions was carried out to increase the cell concentration of A. vinelandii, in order to favor and determine its tolerance to chlorpyrifos and its degradation ability. The culture in shaken flasks, using sucrose as a carbon source, significantly improved the growth compared to media with mannitol. When the strain was cultivated under oxygen-limited (5.5, 11.25 mmol L-1 h-1) and no-oxygen-limited conditions (22 mmol L-1 h-1), the growth parameters were not affected. In cultures in a liquid medium with chlorpyrifos, the bacteria tolerated a high pesticide concentration (500 ppm) and the growth parameters were improved even under conditions with a reduced carbon source (sucrose 2 g L-1). The strain degraded 99.6% of chlorpyrifos at 60 h of cultivation, in co-metabolism with sucrose; notably, A. vinelandii ATCC 12837 reduced by 50% the initial pesticide concentration in only 6 h (DT50).

The dynamics of the roo transposable element in mutation-accumulation lines and segregating populations of Drosophila melanogaster.

We estimated the number of copies for the long terminal repeat (LTR) retrotransposable element roo in a set of long-standing Drosophila melanogaster mutation-accumulation full-sib lines and in two large laboratory populations maintained with effective population size approximately 500, all of them derived from the same isogenic origin. Estimates were based on real-time quantitative PCR and in situ hybridization. Considering previous estimates of roo copy numbers obtained at earlier stages of the experiment, the results imply a strong acceleration of the insertion rate in the accumulation lines. The detected acceleration is consistent with a model where only one (maybe a few) of the approximately 70 roo copies in the ancestral isogenic genome was active and each active copy caused new insertions with a relatively high rate ( approximately 10(-2)), with new inserts being active copies themselves. In the two laboratory populations, however, a stabilized copy number or no accelerated insertion was found. Our estimate of the average deleterious viability effects per accumulated insert [E(s) < 0.003] is too small to account for the latter finding, and we discuss the mechanisms that could contain copy number.

The build up of mutation-selection- drift balance in laboratory Drosophila populations.

The build up of an equilibrium between mutation, selection, and drift in populations of moderate size is an important evolutionary issue, and can be critical in the conservation of endangered populations. We studied this process in two Drosophila melanogaster populations initially lacking genetic variability (C1 and C2) that were subsequently maintained during 431 or 165 generations with effective population size N(e) approximately 500 (estimated by lethal complementation analysis). Each population originated synchronously to a companion set of full-sib mutation accumulation (MA) lines, C1 and MA1 were derived from an isogenic origin and C2 and MA2 from a single MA1 line at generation 265. The results suggest that both C1 and C2 populations were close to the mutation-selection-drift balance for viability and bristle traits, and are consistent with a 2.5-fold increase of the mutation rate in C2 and MA2. Despite this increase, the average panmictic viability in C2 was only slightly below that of C1, indicating that the expressed loads due to segregating deleterious mutation were small, in agreement with the low deleterious mutation rate (0.015-0.045) previously reported for the MA1 lines. In C1, the nonlethal inbreeding depression rate for viability was 30% of that usually estimated in segregating populations. The genetic variance for bristles regenerated in C1 and C2 was moderately smaller than the average value reported for natural populations, implying that they have accumulated a substantial adaptive potential. In light of neutral and selective predictions, these results suggest that bristle additive variance was predominantly due to segregation of mutations with deleterious effects of the order of 10(-3), and is consistent with relatively weak causal stabilizing selection (V(s) approximately 30).

Increase of the spontaneous mutation rate in a long-term experiment with Drosophila melanogaster.

In a previous experiment, the effect of 255 generations of mutation accumulation (MA) on the second chromosome viability of Drosophila melanogaster was studied using 200 full-sib MA1 lines and a large C1 control, both derived from a genetically homogeneous base population. At generation 265, one of those MA1 lines was expanded to start 150 new full-sib MA2 lines and a new C2 large control. After 46 generations, the rate of decline in mean viability in MA2 was approximately 2.5 times that estimated in MA1, while the average degree of dominance of mutations was small and nonsignificant by generation 40 and moderate by generation 80. In parallel, the inbreeding depression rate for viability and the amount of additive variance for two bristle traits in C2 were 2-3 times larger than those in C1. The results are consistent with a mutation rate in the line from which MA2 and C2 were derived about 2.5 times larger than that in MA1. The mean viability of C2 remained roughly similar to that of C1, but the rate of MA2 line extinction increased progressively, leading to mutational collapse, which can be ascribed to accelerated mutation and/or synergy after important deleterious accumulation.

The action of stabilizing selection, mutation, and drift on epistatic quantitative traits.

For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus epistasis (synergistic/antagonistic) among linked or unlinked loci on the distribution of effects and frequencies of segregating loci in populations at the mutation-selection-drift balance. Strong pervasive epistasis did not modify substantially the genetic properties of the trait and, therefore, the most likely explanation for the low amount of variation usually accounted by the loci detected in genome-wide association analyses is that many causal loci will pass undetected. We investigated the impact of epistasis on the changes in genetic variance components when large populations were subjected to successive bottlenecks of different sizes, considering the action of genetic drift, operating singly (D), or jointly with mutation (MD) and selection (MSD). An initial increase of the different components of the genetic variance, as well as a dramatic acceleration of the between-line divergence, were always associated with synergistic epistasis but were strongly constrained by selection.

Faster-X effects in two Drosophila lineages.

Under certain circumstances, X-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. To look for evidence of faster-X evolution, we analyzed the evolutionary rates of coding sequences in two sets of Drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. One of these, the pseudoobscura clade, contains a centric fusion between the ancestral X chromosome and the autosomal arm homologous to 3L in D. melanogaster. This offers an opportunity to study the same loci in both an X-linked and an autosomal context, and to compare these loci with those that are only X-linked or only autosomal. We therefore investigated these clades for evidence of faster-X evolution with respect to nonsynonymous substitutions, finding mixed results. Overall, there was consistent evidence for a faster-X effect in the melanogaster clade, but not in the pseudoobscura clade, except for the comparison between D. pseudoobscura and its close relative, Drosophila persimilis. An analysis of polymorphism data on a set of genes from D. pseudoobscura that evolve rapidly with respect to their protein sequences revealed no evidence for a faster-X effect with respect to adaptive protein sequence evolution; their rapid evolution is instead largely attributable to lower selective constraints. Faster-X evolution in the melanogaster clade was not related to male-biased gene expression; surprisingly, however, female-biased genes showed evidence for faster-X effects, perhaps due to their sexually antagonistic effects in males.

Candidate transcriptomic sources of inbreeding depression in Drosophila melanogaster.

The genomic causes of inbreeding depression are poorly known. Several studies have found widespread transcriptomic alterations in inbred organisms, but it remains unclear which of these alterations are causes of the depression and which are mere responses to the ensuing physiological stress induced by increased homozygosity due to inbreeding. Attempting to differentiate causes from responses, we made a c-DNA microarray analysis of inbreeding depression in Drosophila melanogaster. The rationale of the experiment was that, while depression is a general phenomenon involving reductions in fitness in different inbred lines, its first genetic causes would be different for each inbred line, as they are expected to be caused by the fixation of rare deleterious genes. We took four sets of inbred sublines, each set descending from a different founding pair obtained from a large outbred stock, and compared the expression of the three most depressed sublines and the three least depressed sublines from each set. Many changes in expression were common to all sets, but fourteen genes, grouped in four expression clusters, showed strong set-specific changes, and were therefore possible candidates to be sources of the inbreeding depression observed.

Are transcriptional responses to inbreeding a functional response to alleviate inbreeding depression?

Previous studies addressing the relationship between gene regulation and inbreeding depression did not allow for discerning the changes that alleviate the depression from those that generate it. We directly addressed this question by analyzing changes in gene expression, using Affymetrix 2.0 arrays in Drosophila melanogaster inbred sublines differing in their magnitudes of inbreeding depression relative to the expression in an outbred control. The total number of arrays analyzed was 27, with 9,133 probe sets showing a significant signal of expression. We found that for those genes differentially expressed between inbred and outbred sublines, most of them showed a pattern of expression consistent with a protective role against inbreeding effects. The observed increase in depression was presumably related to an inability of the genome to do the appropriate expression adjustments. Expression changes detected in our study showed a clear specificity of RNA-splicing and energy derivation functions. Thus, it appears that most of the observed changes in gene expression associated with inbreeding may occur predominantly to alleviate inbreeding depression, i.e., as a protection against the effects of inbreeding.

Gene-expression changes caused by inbreeding protect against inbreeding depression in Drosophila.

We present a transcriptomic analysis aimed at investigating whether the changes in gene expression that occur under inbreeding generally reduce or enhance inbreeding depression. Discerning between these two alternatives can be addressed only when both changes in expression due to inbreeding and to inbreeding depression are estimated simultaneously. We used Affymetrix 2.0 arrays to study the changes in gene expression associated with both inbreeding and inbreeding depression for fitness in four sets of inbred sublines of Drosophila melanogaster. We found that for most genes showing changes in expression associated with inbreeding, the least depressed sublines were those showing the largest departures in expression from that of the outbred control. This suggests a pattern consistent with a protective role of expression changes against inbreeding effects, and would reveal a new dimension of the transcriptomics of inbreeding. The variation in depression observed could then be due not only to the genetic damages primarily originating that depression, but also possibly to differences in the ability to carry out the appropriate adjustments in gene expression to cope with the inbreeding. We also found that these expression changes with a putative protective role against inbreeding effects show a clear specificity on RNA synthesis and splicing and energy derivation functions.