Organic C and N stabilization in a forest soil: Evidence from sequential density fractionation

In mineral soil, organic matter (OM) accumulates mainly on and around surfaces of silt- and clay-size particles. When fractionated according to particle density, C and N concentration (per g fraction) and C/N of these soil organo-mineral particles decrease with increasing particle density across soils of widely divergent texture, mineralogy, location, and management. The variation in particle density is explained potentially by two factors: (1) a decrease in the mass ratio of organic to mineral phase of these particles, and (2) variations in density of the mineral phase. The first explanation implies that the thickness of the organic accumulations decreases with increasing particle density. The decrease in C/N can be explained at least partially by especially stable sorption of nitrogenous N-containing compounds (amine, amide, and pyrrole) directly to mineral surfaces, a phenomenon well documented both empirically and theoretically. These peptidic compounds, along with ligand-exchanged carboxylic compounds, could then form a stable inner organic layer onto which other organics could sorb more readily than onto the unconditioned mineral surfaces (“onion” layering model).To explore mechanisms underlying this trend in C concentration and C/N with particle density, we sequentially density fractionated an Oregon andic soil at 1.65, 1.85, 2.00, 2.28, and 2.55 g cm⁻³ and analyzed the six fractions for measures of organic matter and mineral phase properties.All measures of OM composition showed either: (1) a monotonic change with density, or (2) a monotonic change across the lightest fractions, then little change over the heaviest fractions. Total C, N, and lignin phenol concentration all decreased monotonically with increasing density, and ¹⁴C mean residence time (MRT) increased with particle density from ca. 150 years to >980 years in the four organo-mineral fractions. In contrast, C/N, ¹³C and ¹⁵N concentration all showed the second pattern. All these data are consistent with a general pattern of an increase in extent of microbial processing with increasing organo-mineral particle density, and also with an “onion” layering model.X-ray diffraction before and after separation of magnetic materials showed that the sequential density fractionation (SDF) isolated pools of differing mineralogy, with layer-silicate clays dominating in two of the intermediate fractions and primary minerals in the heaviest two fractions. There was no indication that these differences in mineralogy controlled the differences in density of the organo-mineral particles in this soil. Thus, our data are consistent with the hypothesis that variation in particle density reflects variation in thickness of the organic accumulations and with an “onion” layering model for organic matter accumulation on mineral surfaces. However, the mineralogy differences among fractions made it difficult to test either the layer-thickness or “onion” layering models with this soil. Although SDF isolated pools of distinct mineralogy and organic-matter composition, more work will be needed to understand mechanisms relating the two factors.     

Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine

In mammalian cells, repair of DNA double-strand breaks (DSBs) by nonhomologous end-joining (NHEJ) is critical for genome stability. Although the end-bridging and ligation steps of NHEJ have been reconstituted in vitro, little is known about the end-processing reactions that occur before ligation. Recently, functionally homologous end-bridging and ligation activities have been identified in prokarya. Consistent with its homology to polymerases and nucleases, we demonstrate that DNA ligase D from Mycobacterium tuberculosis (Mt-Lig) possesses a unique variety of nucleotidyl transferase activities, including gap-filling polymerase, terminal transferase, and primase, and is also a 3' to 5' exonuclease. These enzyme activities allow the Mt-Ku and Mt-Lig proteins to join incompatible DSB ends in vitro, as well as to reconstitute NHEJ in vivo in yeast. These results demonstrate that prokaryotic Ku and ligase form a bona fide NHEJ system that encodes all the recognition, processing, and ligation activities required for DSB repair.     

Discovery and directed evolution of a glyphosate tolerance gene

The herbicide glyphosate is effectively detoxified by N-acetylation. We screened a collection of microbial isolates and discovered enzymes exhibiting glyphosate N-acetyltransferase (GAT) activity. Kinetic properties of the discovered enzymes were insufficient to confer glyphosate tolerance to transgenic organisms. Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM-1 min-1 to 8320 mM-1 min-1. From the fifth iteration and beyond, GAT enzymes conferred increasing glyphosate tolerance to Escherichia coli, Arabidopsis, tobacco, and maize. Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops.     

Rise and fall of species occupancy in Cenozoic fossil mollusks

In the time between speciation and extinction, a species' ecological and biogeographic footprint-its occupancy-will vary in response to macroecological drivers and historical contingencies. Despite their importance for understanding macroecological processes, general patterns of long-term species occupancy remain largely unknown. We documented the occupancy histories of Cenozoic marine mollusks from New Zealand. For both genera and species, these show a distinct pattern of increase to relatively short-lived peak occupancy at mid-duration, followed by a decline toward extinction. Thus, species at greatest risk for extinction are those that have already been in decline for a substantial period of time. This pattern of protracted rise and fall stands in contrast to that of incumbency, insofar as species show no general tendency to stay near maximal occupancy once established.     

A protein sensor for siRNA asymmetry

To act as guides in the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be unwound into their component strands, then assembled with proteins to form the RNA-induced silencing complex (RISC), which catalyzes target messenger RNA cleavage. Thermodynamic differences in the base-pairing stabilities of the 5' ends of the two approximately 21-nucleotide siRNA strands determine which siRNA strand is assembled into the RISC. We show that in Drosophila, the orientation of the Dicer-2/R2D2 protein heterodimer on the siRNA duplex determines which siRNA strand associates with the core RISC protein Argonaute 2. R2D2 binds the siRNA end with the greatest double-stranded character, thereby orienting the heterodimer on the siRNA duplex. Strong R2D2 binding requires a 5'-phosphate on the siRNA strand that is excluded from the RISC. Thus, R2D2 is both a protein sensor for siRNA thermodynamic asymmetry and a licensing factor for entry of authentic siRNAs into the RNAi pathway.     

Energy and Carbon Costs of Selected Cow-Calf Systems

Fossil fuel-derived inputs can increase cow-calf production per unit of land or labor but can raise financial and environmental concerns. Eleven US cow-calf systems from nine ecological regions in Iowa, South Dakota, Tennessee, and Texas were analyzed to determine quantities of energy used and carbon (C) emitted due to fossil fuel use (excluding emissions from soils and biota) and to determine how management and environment influenced those quantities. Total energy and C cost, calculated cow^?1 or ha^?1, were highly correlated (0.99). Energy use cow^?1 and ha^?1 varied greatly across systems, ranging from 3 000 to 12 600 megajoules (MJ) · cow^?1 · yr^?1 and from 260 to 20 800 MJ · ha^?1 · yr^?1. As stocking rate increased, MJ · cow^?1 increased at an increasing rate. Differences in quantity of fertilizer accounted for most variation in energy use. Fertilizer allowed higher stocking rates but reduced energy efficiency of liveweight marketed. Compared to intensive, higher stocking rate systems, rangeland systems based on native or naturalized forages used little or no fertilizer, but used more energy cow^?1 for crude protein (CP) supplementation, fencing, and pickup trucks. Across all systems, energy used to produce winter feed ranged from 0% to 46% of total energy. Northern systems used higher percentages of total energy for winter feed and fed for more days year^?1, but southern systems that included large amounts of bermudagrass (Cynodon dactylon L.) hay used the most MJ · cow^?1 for winter feed. Systems with high MJ · cow^?1 were vulnerable to shocks in energy prices. Reducing energy use and C emissions from cow-calf operations is possible, especially by reducing fertilizer and hay use, but would likely reduce productivity ha^?1. Forages with high nitrogen use efficiency, locally adapted plants and animals, and replacement of hay with unfertilized dormant forage and CP supplementation could reduce energy use.     

Primary lacrimal gland adenocarcinoma of the third eyelid in a horse

A 5-year-old Draft Horse gelding presented for evaluation of a large, fleshy, ulcerated third eyelid mass OD of 3 weeks duration. Complete ophthalmic examination, ocular ultrasound and skull radiographs revealed a large soft-tissue mass involving the entire third eyelid OD and extending into the ventral right orbit to the level of the globe equator. No other abnormalities were noted on physical or ophthalmic examination. Surgical removal via exenteration was performed 3 months after initial presentation. A lacrimal adenocarcinoma of the third eyelid was diagnosed based on histopathology. Concurrent asymptomatic intra-ductal and intra-acinar Demodex caballi parasites were found in the eyelid sebaceous glands, likely as an incidental finding. No tumor recurrence or metastasis has occurred 12 months after excision. To the author's knowledge, this case is the first reported primary lacrimal adenocarcinoma in a horse. Complete surgical excision was curative.     

Insecticidal potency of novel compounds on multiple insect species of medical and veterinary importance

BACKGROUND: Vector‐borne diseases continue to present significant threats to human, animal and plant health. Mosquitoes, houseflies, sand flies and stable flies are well‐known vectors of several human and animal pathogens. The toxicity of selected semiochemicals with molecular structures indicative of insecticidal activity was determined against these insect species with the aim of developing novel insecticides toxic to multiple insect species. RESULTS: Three semiochemicals, namely beta‐damascone, cyclemone A and melafleur, showed remarkable toxicity to three mosquitoes, Aedes aegypti L., Ae. albopictus (Skuse) and Anopheles quadrimaculatus Say, the housefly, Musca domestica L., the stable fly, Stomoxys calcitrans L., and the sand fly, Lutzomyia shannoni (Dyar). The chemicals were equally toxic to several field‐collected permethrin‐tolerant housefly strains. When formulated as 500 mL L^?1 emulsifiable concentrates, the chemicals demonstrated stability and toxicity on filter paper and camouflage military fabrics, with persistence up to 8 days under laboratory conditions. The chemicals were equally effective under field conditions when evaluated on unpainted plywood panels, although a higher dosage was required under field conditions to achieve similar efficacy. CONCLUSION: Laboratory quantification of LC₅₀ values and field efficacy of three semiochemicals as formulated compounds on mosquitoes, houseflies, stable flies and sand flies showed that these semiochemicals could serve as potent insecticides for multiple insect species. Copyright © 2010 Society of Chemical Industry