Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.     

A CBS domain-containing pyrophosphatase of Moorella thermoacetica is regulated by adenine nucleotides

CBS (cystathionine beta-synthase) domains are found in proteins from all kingdoms of life, and point mutations in these domains are responsible for a variety of hereditary diseases in humans; however, the functions of CBS domains are not well understood. In the present study, we cloned, expressed in Escherichia coli, and characterized a family II PPase (inorganic pyrophosphatase) from Moorella thermoacetica (mtCBS-PPase) that has a pair of tandem 60-amino-acid CBS domains within its N-terminal domain. Because mtCBS-PPase is a dimer and requires transition metal ions (Co2+ or Mn2+) for activity, it resembles common family II PPases, which lack CBS domains. The mtCBS-PPase, however, has lower activity than common family II PPases, is potently inhibited by ADP and AMP, and is activated up to 1.6-fold by ATP. Inhibition by AMP is competitive, whereas inhibition by ADP and activation by ATP are both of mixed types. The nucleotides are effective at nanomolar (ADP) or micromolar concentrations (AMP and ATP) and appear to compete for the same site on the enzyme. The nucleotide-binding affinities are thus 100-10000-fold higher than for other CBS-domain-containing proteins. Interestingly, genes encoding CBS-PPase occur most frequently in bacteria that have a membrane-bound H+-translocating PPase with a comparable PP(i)-hydrolysing activity. Our results suggest that soluble nucleotide-regulated PPases act as amplifiers of metabolism in bacteria by enhancing or suppressing ATP production and biosynthetic reactions at high and low [ATP]/([AMP]+[ADP]) ratios respectively.     

A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows

We developed a method for studying the synchrony of behaviour based on calculations of overdispersion of a binomial process. The lying behaviour of cows was investigated under two different housing units inside the same barn. The first unit housed 30 cows undergoing conventional milking and the second unit housed 27 cows undergoing automatic milking. The lying behaviour of the cows was observed over 3 weeks in 12 periods of 6 h each. Every 5 min, we counted the number of cows lying down in the cubicles. As external cues, like feeding and conventional milking, can promote synchrony in dairy cows, we expected that cows conventionally milked would show more behavioural synchrony than automatically milked cows. Cows lied down synchronously in both units (overdispersion 1.67, P < 0.01). Lying synchrony tended to be slightly bigger in automatically than in conventionally milked cows (overdispersion 1.76 v. 1.58, P = 0.09), although the proportion of cows lying down was on average greater in conventionally than in automatically milked cows (60.7% v. 45.6%). This suggests that synchronized lying behaviour in cows is a constant phenomenon that depends on social facilitation rather than on external cues. The overdispersion index appears to be a useful tool for studying the synchrony of animal behaviour when observations are made at the group level.     

Spatial frequency-based analysis of mean red blood cell speed in single microvessels: investigation of microvascular perfusion in rat cerebral cortex

Background

Our previous study has shown that prenatal exposure to X-ray irradiation causes cerebral hypo-perfusion during the postnatal development of central nervous system (CNS). However, the source of the hypo-perfusion and its impact on the CNS development remains unclear. The present study developed an automatic analysis method to determine the mean red blood cell (RBC) speed through single microvessels imaged with two-photon microscopy in the cerebral cortex of rats prenatally exposed to X-ray irradiation (1.5 Gy).

Methodology/Principal Findings

We obtained a mean RBC speed (0.9±0.6 mm/sec) that ranged from 0.2 to 4.4 mm/sec from 121 vessels in the radiation-exposed rats, which was about 40% lower than that of normal rats that were not exposed. These results were then compared with the conventional method for monitoring microvascular perfusion using the arteriovenous transit time (AVTT) determined by tracking fluorescent markers. A significant increase in the AVTT was observed in the exposed rats (1.9±0.6 sec) as compared to the age-matched non-exposed rats (1.2±0.3 sec). The results indicate that parenchyma capillary blood velocity in the exposed rats was approximately 37% lower than in non-exposed rats.

Conclusions/Significance

The algorithm presented is simple and robust relative to monitoring individual RBC speeds, which is superior in terms of noise tolerance and computation time. The demonstrative results show that the method developed in this study for determining the mean RBC speed in the spatial frequency domain was consistent with the conventional transit time method.     

Trace fossils as indicators of environmental change in Holocene sediments of the Archipelago Sea, northern Baltic Sea

Biogenic structures in Holocene sediments from the Archipelago Sea, northern Baltic Sea, were characterized through the analysis of X-ray images of four cores collected from water depths between 32 and 66 m. In the area, initial colonization of endobenthic invertebrates occurred at 7800 ± 80 calendar years BP. The trace assemblage at this level is low-diversity, small-diameter, shallowly tiered, and Palaeophycus-dominated; rare Arenicolites are also observed. Early colonization coincides with increasing marine influence in the post-glacial lacustrine setting just before the dramatic onset of brackish-water conditions established after 7600 BP. The post-incursion brackish-water assemblage possesses a higher diversity of traces (Planolites, Arenicolites, Lockeia, Teichichnus), which is taken to reflect the enhanced salinity and trophic state of the basin. The shift from Palaeophycus-mottling to a Planolites-dominated fabric represents changed behavioural patterns in the endobenthic community due to changed substrate properties. The ethology of the succeeding trace assemblage also represents a switch from domicile-based activities, such as predation, scavenging and interface-dominated deposit feeding to shallow-tier deposit feeding. Finally, traces are excluded from thinly laminated intervals, demonstrating that seafloor oxygen deficiency commonly reached levels that were detrimental to colonization of the sediment substrate.     

Enhanced activity of hyperthermostable Pyrococcus horikoshii endoglucanase in superbase ionic liquids

Biotechnology Letters - Ionic liquids (ILs) that dissolve biomass are harmful to the enzymes that degrade lignocellulose. Enzyme hyperthermostability promotes a tolerance to ILs. Therefore, the...     

Development of recombinant antibody-based enzyme-linked immunosorbent assay (ELISA) for the detection of skatole

The occurrence of boar taint and the European Commission recommendation to discontinue the surgical castration of pigs by the year 2018 creates an urgent need for new analytical methods that are simple, affordable, and suitable for field testing. We describe the generation and engineering of a skatole-specific antibody derived from a synthetic antibody library and the development of ELISA for its detection. The immunoassay is capable of detecting skatole with IC50 of 222 μg L⁻¹, which is within the analytical threshold level suggested for skatole, and with low cross-reactivity interference from other indolic compounds.     

DNA family shuffling within the chicken avidin protein family - A shortcut to more powerful protein tools

Avidins represent an interesting group of proteins showing high structural similarity and ligand-binding properties but low similarity in primary structure. In this study, we show that it is possible to create functional chimeric proteins from the avidin protein family when applying DNA family shuffling to the genes of the avidin protein family: avidin, avidin related gene 2 and biotin-binding protein A. The novel chimeric proteins were selected by phage display biopanning against biotin, and the selected enriched proteins were characterized, displaying diverse features distinct from the parental genes, including binding to cysteine.     

Sequential Posttranslational Modifications Program FEN1 Degradation during Cell-Cycle Progression

We propose that cell-cycle-dependent timing of FEN1 nuclease activity is essential for cell-cycle progression and the maintenance of genome stability. After DNA replication is complete at the exit point of the S phase, removal of excess FEN1 may be crucial. Here, we report a mechanism that controls the programmed degradation of FEN1 via a sequential cascade of posttranslational modifications. We found that FEN1 phosphorylation stimulated its SUMOylation, which in turn stimulated its ubiquitination and ultimately led to its degradation via the proteasome pathway. Mutations or inhibitors that blocked the modification at any step in this pathway suppressed FEN1 degradation. Critically, the presence of SUMOylation- or ubiquitination-defective, nondegradable FEN1 mutant protein caused accumulation of Cyclin B, delays in the G1 and G2/M phases, and polyploidy. These findings may represent a newly identified regulatory mechanism used by cells to ensure precise cell-cycle progression and to prevent transformation.