Influence of hydrological connectivity of riverine wetlands on nitrogen removal via denitrification

Wetland ecosystems in agricultural areas often become progressively more isolated from main water bodies. Stagnation favors the accumulation of organic matter as the supply of electron acceptors with water renewal is limited. In this context it is expected that nitrogen recycling prevails over nitrogen dissipation. To test this hypothesis, denitrification rates, fluxes of dissolved oxygen (SOD), inorganic carbon (DIC) and nitrogen and sediment features were measured in winter and summer 2007 on 22 shallow riverine wetlands in the Po River Plain (Northern Italy). Fluxes were determined from incubations of intact cores by measurement of concentration changes or isotope pairing in the case of denitrification. Sampled sites were eutrophic to hypertrophic; 10 were connected and 12 were isolated from the adjacent rivers, resulting in large differences in nitrate concentrations in the water column (from <5 to 1,133 μM). Benthic metabolism and denitrification rates were investigated by two overarching factors: season and hydrological connectivity. SOD and DIC fluxes resulted in respiratory quotients greater than one at most sampling sites. Sediment respiration was coupled to both ammonium efflux, which increased from winter to summer, and nitrate consumption, with higher rates in river-connected wetlands. Denitrification rates measured in river-connected wetlands (35–1,888 μmol N m^?2 h^?1) were up to two orders of magnitude higher than rates measured in isolated wetlands (2–231 μmol N m^?2 h^?1), suggesting a strong regulation of the process by nitrate availability. These rates were also significantly higher in summer (9–1,888 μmol N m^?2 h^?1) than in winter (2–365 μmol N m^?2 h^?1). Denitrification supported by water column nitrate (D_W) accounted for 60–100% of total denitrification (Dtot); denitrification coupled to nitrification (D_N) was probably controlled by limited oxygen availability within sediments. Denitrification efficiency, calculated as the ratio between N removal via denitrification and N regeneration, and the relative role of denitrification for organic matter oxidation, were high in connected wetlands but not in isolated sites. This study confirms the importance of restoring hydraulic connectivity of riverine wetlands for the maintenance of important biogeochemical functions such as nitrogen removal via denitrification.     

Discovery of a novel styrene monooxygenase originating from the metagenome

Oxygenases form an interesting class of biocatalysts, as they typically perform oxygenations with exquisite chemo-, regio-, and/or enantioselectivity. It has been observed that, once heterologously expressed in Escherichia coli, some oxygenases are able to form the blue pigment indigo. We have exploited this characteristic to screen a metagenomic library derived from loam soil and identified a novel oxygenase. This oxygenase shows 50% sequence identity with styrene monooxygenases from pseudomonads (StyA). Only a limited number of homologs can be found in the genome sequence database, indicating that this biocatalyst is a member of a relatively small family of bacterial monooxygenases. The newly identified monooxygenase catalyzes the epoxidation of styrene and styrene derivatives and forms the corresponding (S)-epoxides with excellent enantiomeric excess [e.g., (S)-styrene oxide is formed with >99% enantiomeric excess, ee] and therefore is named styrene monooxgenase subunit A (SmoA). SmoA shows high enantioselectivity towards aromatic sulfides [e.g., (R)-ethyl phenyl sulfoxide is formed with 92% ee]. This excellent enantioselectivity in combination with the moderate sequence identity forms a clear indication that SmoA from a metagenomic origin represents a new enzyme within the small family of styrene monooxygenases.     

INCREASED RESIDUAL VARIANCE AT DEVELOPMENTAL SWITCH POINTS: STATISTICAL ARTIFACT OR INDICATOR OF EXPOSED GENOTYPIC INFLUENCE?

Discussing the organization of developmental switches, West-Eberhard (2003) proposed the use of regression residual plots to locate the neutral point of the switch, which is characterized by maximum genotypic influence on the resulting phenotype. However, statistical artifacts due to measurement error in nonlinear models might account for a substantial proportion of the increase of residuals variance at the switch point. Simulations based on field data show that increases in residual variance occur as artifacts when normal amounts of measurement error are present, even in absence of any genotypic variance. The results suggest that interpretation of nonlinear variation in thresold traits is problematic and requires considering this statistical effect. A method to estimate the weight of genotypic contribution to residual variance is proposed, and its assumptions and limitations are discussed.     

Bacterial colonization of a fumigated alkaline saline soil

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m^?1, and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8 %) compared to the unfumigated soil (34.2 %), while that of the Bacteroidetes decreased from 16.2 % in the unfumigated soil to 8.8 % in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7 % in the unfumigated soil to 25.7 %. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.     

The height of Tennessee convicts: another piece of the “antebellum puzzle”

Average height of the free population in the United States born in the mid-1830s began to decline despite growing per capita incomes. Explanations for this "antebellum puzzle" revolve around a possibly deteriorating disease environment promoted by urban agglomeration and increases in the relative price of protein-rich foods. However, several groups were immune to the effect, including members of the middle class, whose income was high enough, and increased enough to overcome the adverse developments and maintain their nutritional status. Although at the opposite end of the social spectrum, the height of male slaves also increased, as it was in their owners' interest to raise their slaves' food allotments. The height of Tennessee convicts, analyzed in this article, also increased in the late-1830s, being the third exception to the "antebellum puzzle." Mid-19th century Tennessee was integrated into interstate commerce in cotton and tobacco and experienced considerable movement of people who would have brought with them diseases from elsewhere, hence, it would have been integrated into the US disease pool, and the fact that heights did not decline in the 1830s is therefore an indication that the antebellum puzzle cannot be explained exclusively by the spread of diseases. Yet, Tennessee's economy was quite different to that of the rest of the country. Although it did export live swine to the South, these exports did not increase during the antebellum decades. Hence, Tennessee remained self-sufficient in pork, and consumption of pork did not decline. Thus, the evidence presented here is consistent with the economic interpretation of the "antebellum puzzle": self-sufficiency in protein production protected even the members of the lower-classes of Tennessee from the negative externalities associated with the onset of industrialization.     

Nitric Oxide Mediates the Glutamate-dependent Pathway for Neurotransmission in Sepia officinalis Chromatophore Organs

Chromatophore organs are complex and unique structures responsible for the variety of body coloration patterns used by cephalopods to communicate and camouflage. They are formed by a pigment-containing cytoelastic sacculus, surrounded by muscle fibers directly innervated from the brain. Muscle contraction and relaxation are responsible for expansion and retraction of the pigment-containing cell. Their functioning depends on glutamate and Phe-Met-Arg-Phe-NH₂-related peptides, which induce fast and slow cell expansion, respectively, and 5-hydroxytryptamine, which induces retraction. Apart from these three substances and acetylcholine, which acts presynaptically, no other neuroactive compounds have so far been found to be involved in the neuroregulation of chromatophore physiology, and the detailed signaling mechanisms are still little understood. Herein, we disclose the role of nitric oxide (NO) as mediator in one of the signaling pathways by which glutamate activates body patterning. NO and nitric-oxide synthase have been detected in pigment and muscle fibers of embryo, juvenile, and adult chromatophore organs from Sepia officinalis. NO-mediated Sepia chromatophore expansion operates at slower rate than glutamate and involves cGMP, cyclic ADP-ribose, and ryanodine receptor activation. These results demonstrate for the first time that NO is an important messenger in the long term maintenance of the body coloration patterns in Sepia.     

European Roe Deer Increase Vigilance When Faced with Immediate Predation Risk by Eurasian Lynx

Prey animals must balance antipredatory behaviour with foraging behaviour. According to the risk allocation hypothesis, prey increase antipredatory behaviour and reduce foraging activity during pulses of high risk, but with continuous risk, other activities must continue and antipredatory behaviour decreases despite the risk. We studied the impact of lynx presence on the vigilance behaviour of wild roe deer under conditions of (i) a pulsed elevated risk by experimentally spreading lynx urine as an olfactory cue, and (ii) continuous risk by comparing an area where lynx was eradicated 160 years ago to an area where lynx has been re‐introduced 30 years ago. Roe deer were extremely vigilant in response to the predator olfactory cue; however, roe deer vigilance did not differ measurably among areas with or without potential lynx presence. Deer were more vigilant before sunset than during the night at both study areas, probably due to long‐term adaptation of roe deer to human hunting during daytime. Vigilance decreased from August to September even though activity of lynx increases in autumn, which may be a result either of increased foraging due to decrease in food quality in autumn, or of changes in social organization of the deer. Our results suggested that the degree of vigilance depends on environmental cues. We found that roe deer respond to lynx urine despite a long absence of lynx in the ecosystem. Our results support the risk allocation hypothesis for responses to pulses of high risk but not for responses to continuous elevated levels of risk.     

Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer

The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array, fluorescent in situ hybridization and polymerase chain reaction-based techniques, we inferred the fine structure of MYC-containing dmin/hsr amplicons harboring sequences from several different chromosomes in seven tumor cell lines, and characterized an unprecedented number of hsr insertion sites. Local chromosome shattering involving a single-step catastrophic event (chromothripsis) was recently proposed to explain clustered chromosomal rearrangements and genomic amplifications in cancer. Our bioinformatics analyses based on the listed criteria to define chromothripsis led us to exclude it as the driving force underlying amplicon genesis in our samples. Instead, the finding of coexisting heterogeneous amplicons, differing in their complexity and chromosome content, in cell lines derived from the same tumor indicated the occurrence of a multi-step evolutionary process in the genesis of dmin/hsr. Our integrated approach allowed us to gather a complete view of the complex chromosome rearrangements occurring within MYC amplicons, suggesting that more than one model may be invoked to explain the origin of dmin/hsr in cancer. Finally, we identified PVT1 as a target of fusion events, confirming its role as breakpoint hotspot in MYC amplification.