Bacterial alginate production: an overview of its biosynthesis and potential industrial production

Alginate is a linear polysaccharide that can be used for different applications in the food and pharmaceutical industries. These polysaccharides have a chemical structure composed of subunits of (1–4)-β-d-mannuronic acid (M) and its C-5 epimer α-l-guluronic acid (G). The monomer composition and molecular weight of alginates are known to have effects on their properties. Currently, these polysaccharides are commercially extracted from seaweed but can also be produced by Azotobacter vinelandii and Pseudomonas spp. as an extracellular polymer. One strategy to produce alginates with different molecular weights and with reproducible physicochemical characteristics is through the manipulation of the culture conditions during fermentation. This mini-review provides a comparative analysis of the metabolic pathways and molecular mechanisms involved in alginate polymerization from A. vinelandii and Pseudomonas spp. Different fermentation strategies used to produce alginates at a bioreactor laboratory scale are described.     

Insights into regional patterns of Amazonian forest structure,diversity, and dominance from three large terra-firme forest dynamics plots

We analyze forest structure, diversity, and dominance in three large-scale Amazonian forest dynamics plots located in Northwestern (Yasuni and Amacayacu) and central (Manaus) Amazonia, to evaluate their consistency with prevailing wisdom regarding geographic variation and the shape of species abundance distributions, and to assess the robustness of among-site patterns to plot area, minimum tree size, and treatment of morphospecies. We utilized data for 441,088 trees (DBH ≥1 cm) in three 25-ha forest dynamics plots. Manaus had significantly higher biomass and mean wood density than Yasuni and Amacayacu. At the 1-ha scale, species richness averaged 649 for trees ≥1 cm DBH, and was lower in Amacayacu than in Manaus or Yasuni; however, at the 25-ha scale the rankings shifted, with Yasuni < Amacayacu < Manaus. Within each site, Fisher’s alpha initially increased with plot area to 1–10 ha, and then showed divergent patterns at larger areas depending on the site and minimum size. Abundance distributions were better fit by lognormal than by logseries distributions. Results were robust to the treatment of morphospecies. Overall, regional patterns in Amazonian tree species diversity vary with the spatial scale of analysis and the minimum tree size. The minimum area to capture local diversity is 2 ha for trees ≥1 cm DBH, or 10 ha for trees ≥10 cm DBH. The underlying species abundance distribution for Amazonian tree communities is lognormal, consistent with the idea that the rarest species have not yet been sampled. Enhanced sampling intensity is needed to fill the still large voids we have in plant diversity in Amazon forests.     

Testing genotyping strategies for ultra‐deep sequencing of a co‐amplifying gene family: MHC class I in a passerine bird

Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co‐amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra‐deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500–20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within‐method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co‐amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co‐amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage.     

The burrow ofDasypus hybridus (Cingulata: Dasypodidae)

Dasypus hybridus (Desmarest, 1804) inhabits open fields in southern South America. Burrows ofD. hybridus were cylindrical with a conical end. They had an entrance and a single tunnel without branches. Three locations of the burrows in the terrain were detected: in banks of dried waterways, near rocks, and in open field. The orientation of 29 burrow mouths was not random and, although they did not point to any cardinal point, in particular there was a strong tendency to avoid the south quadrant. In a sample area of 90 × 140 m, burrow mouths were arranged in a random spatial pattern with a density of 25.4 burrows per ha. Great variation in burrow length was found (118.8 ± 105.69 cm, CV = 89.0%). Tunnels may be used as refuges and/or for thermoregulation. The orientation of burrow mouths can also be related to thermoregulation as tunnels are covered from dominant winds, and, for many hours every day, the temperature at the mouths can be influenced by insolation. The possible existence of shelter-burrows and resting-burrows is discussed.     

Optimisation of medium composition for clavulanic acid production by Streptomyces clavuligerus

Among four different commercially available nitrogen sources containing soybean derivatives, a protein extract of soybean gave the highest yield for clavulanic acid production by Streptomyces clavuligerus. A statistical method based on factorial design of experiments was applied to optimise the medium. An empirical model was obtained by applying response surface statistical analysis. The analysis of variance showed that concentrations of protein extract of soybean and glycerol and the interaction between these two variables were significant at 95% level of confidence. The maximum clavulanic acid concentration obtained in 72 h was 1.2 g l^–1.     

Combining field experiments and predictive models to assess potential for increased plant diversity to climate‐proof intensive agriculture

Agricultural production systems face increasing threats from more frequent and extreme weather fluctuations associated with global climate change. While there is mounting evidence that increased plant community diversity can reduce the variability of ecosystem functions (such as primary productivity) in the face of environmental fluctuation, there has been little work testing whether this is true for intensively managed agricultural systems. Using statistical modeling techniques to fit environment–productivity relationships offers an efficient means of leveraging hard‐won experimental data to compare the potential variability of different mixtures across a wide range of environmental contexts. We used data from two multiyear field experiments to fit climate–soil–productivity models for two pasture mixtures under intensive grazing—one composed of two drought‐sensitive species (standard), and an eight‐species mixture including several drought‐resistant species (complex). We then used these models to undertake a scoping study estimating the mean and coefficient of variation (CV) of annual productivity for long‐term climate data covering all New Zealand on soils with low, medium, or high water‐holding capacity. Our results suggest that the complex mixture is likely to have consistently lower CV in productivity, irrespective of soil type or climate regime. Predicted differences in mean annual productivity between mixtures were strongly influenced by soil type and were closely linked to mean annual soil water availability across all soil types. Differences in the CV of productivity were only strongly related to interannual variance in water availability for the lowest water‐holding capacity soil. Our results show that there is considerable scope for mixtures including drought‐tolerant species to enhance certainty in intensive pastoral systems. This provides justification for investing resources in a large‐scale distributed experiment involving many sites under different environmental contexts to confirm these findings.     

c-Myc Regulates Cyclin D-Cdk4 and -Cdk6 Activity but Affects Cell Cycle Progression at Multiple Independent Points

c-myc is a cellular proto-oncogene associated with a variety of human cancers and is strongly implicated in the control of cellular proliferation, programmed cell death, and differentiation. We have previously reported the first isolation of a c-myc-null cell line. Loss of c-Myc causes a profound growth defect manifested by the lengthening of both the G1 and G2 phases of the cell cycle. To gain a clearer understanding of the role of c-Myc in cellular proliferation, we have performed a comprehensive analysis of the components that regulate cell cycle progression. The largest defect observed in c-myc-/- cells is a 12-fold reduction in the activity of cyclin D1-Cdk4 and -Cdk6 complexes during the G0-to-S transition. Downstream events, such as activation of cyclin E-Cdk2 and cyclin A-Cdk2 complexes, are delayed and reduced in magnitude. However, it is clear that c-Myc affects the cell cycle at multiple independent points, because restoration of the Cdk4 and -6 defect does not significantly increase growth rate. In exponentially cycling cells the absence of c-Myc reduces coordinately the activities of all cyclin-cyclin-dependent kinase complexes. An analysis of cyclin-dependent kinase complex regulators revealed increased expression of p27(KIP1) and decreased expression of Cdk7 in c-myc-/- cells. We propose that c-Myc functions as a crucial link in the coordinate adjustment of growth rate to environmental conditions.