DNA topoisomerases participate in fragility of the oncogene RET

Fragile site breakage was previously shown to result in rearrangement of the RET oncogene, resembling the rearrangements found in thyroid cancer. Common fragile sites are specific regions of the genome with a high susceptibility to DNA breakage under conditions that partially inhibit DNA replication, and often coincide with genes deleted, amplified, or rearranged in cancer. While a substantial amount of work has been performed investigating DNA repair and cell cycle checkpoint proteins vital for maintaining stability at fragile sites, little is known about the initial events leading to DNA breakage at these sites. The purpose of this study was to investigate these initial events through the detection of aphidicolin (APH)-induced DNA breakage within the RET oncogene, in which 144 APHinduced DNA breakpoints were mapped on the nucleotide level in human thyroid cells within intron 11 of RET, the breakpoint cluster region found in patients. These breakpoints were located at or near DNA topoisomerase I and/or II predicted cleavage sites, as well as at DNA secondary structural features recognized and preferentially cleaved by DNA topoisomerases I and II. Co-treatment of thyroid cells with APH and the topoisomerase catalytic inhibitors, betulinic acid and merbarone, significantly decreased APH-induced fragile site breakage within RET intron 11 and within the common fragile site FRA3B. These data demonstrate that DNA topoisomerases I and II are involved in initiating APH-induced common fragile site breakage at RET, and may engage the recognition of DNA secondary structures formed during perturbed DNA replication

YIELD GUARANTEES AND THE PRODUCER WELFARE BENEFITS OF CROP INSURANCE

Crop yield and revenue insurance products with coverage based on actual production history (APH) yields dominate the U.S. Federal Crop Insurance Program. The APH yield, which plays a critical role in determining the coverage offered to producers, is based on a small sample of historical yields for the insured unit. The properties of this yield measure are critical in determining the value of the insurance to producers. Sampling error in APH yields has the potential to lead to over-insurance in some years and under-insurance in other years. Premiums, which are in part determined by the ratio of the APH yield to the county reference yield, are also affected by variations in APH yields. Congress has enacted two measures, yield substitution and yield floors, that are intended to limit the degree to which sampling error can reduce the insurance guarantee and producer welfare. We examine the impact of sampling error and related policy provisions for Texas cotton, Kansas wheat, and Illinois corn. The analysis is conducted using county level yield data from the National Agricultural Statistics Service and individual insured-unit-level yield data obtained from the Risk Management Agency’s insurance database. Our findings indicate that sampling error in APH yields has the potential to reduce producer welfare and that the magnitude of this effect differs substantially across crops. The yield substitution and yield floor provisions reduce the negative impact of sampling error but also bias guarantees upward, leading to increased government cost of the insurance programs.Actual Production History, Crop Insurance, Sampling Error, Yield Guarantee, Production Economics, Risk and Uncertainty,

Using [delta] ph as a geochemical index of illite neoformation in saprolite

Sal pH is routinely measured for agronomic purposes. When the difference between KCI pH and H2O pH, or ApH, yields positive values, it is used by soil scientists as a classification criterion for identifying anionic subgroups according to the Soil Taxonomy or geric properties according to the WRB. Negative values have not been granted much attention. Here we focus on the occurrence of highly negative ApH values in the weathering zone of profiles developed on gneiss in semiarid Northeast Brazil and semiarid South India and interpret them as proxies of a geochemical weathering process involving the neoformation of illite. Detailed optical, chemical and mineralogical characterizations involving scanning electron microscopy coupled with X-ray element mapping demonstrate the neoformation of illite inside plagioclase feldspar crystals after their partial dissolution. This study thus reveals that meteoric weathering is capable of producing Mite not only from mica, Le., by a transformation process, but also within non-alkali feldspar by a neoformation process. The ApH is shown to be a good proxy for detecting such weathering signatures because the recently neoformed Mate flakes, which present a significant compositional deficit in K, reveal their presence by a detectable uptake of K from the KCI solution. This finding changes the perspective over the origin of illite in continental environments, which has most commonly been attributed to hydrothermal processes. (Texte intégral

Effect of stocking density of fish on water quality and growth performance of European Carp and leafy vegetables in a low-tech aquaponic system

Aquaponics (AP) is a semi-closed system of food production that combines aquaculture and hydroponics and represents a new agricultural system integrating producers and consumers. The aim of this study was to test the effect of stocking densities (APL, 2.5 kg m-3; APH, 4.6 kg m-3) on water quality, growth performance of the European Carp (Cyprinus carpio L.), and yield of leafy vegetables (catalogna, lettuce, and Swiss Chard) in a low-technology AP pilot system compared to a hydroponic cultivation. The AP daily consumption of water due to evapotranspiration was not different among treatments with an average value of 8.2 L d-1, equal to 1.37% of the total water content of the system. Dissolved oxygen was significantly (p < 0.05) different among treatments with the lowest median value recorded with the highest stocking density of fish (5.6 mg L-1) and the highest median value in the hydroponic control (8.7 mg L-1). Marketable yield of the vegetables was significantly different among treatments with the highest production in the hydroponic control for catalogna (1.2 kg m-2) and in the APL treatment for Swiss Chard (5.3 kg m-2). The yield of lettuce did not differ significantly between hydroponic control and APL system (4.0 kg m-2 on average). The lowest production of vegetables was obtained in the APH system. The final weight (515 g vs. 413 g for APL and APH, respectively), specific growth rate (0.79% d-1 vs. 0.68% d-1), and feed conversion (1.55 vs. 1.86) of European Carp decreased when stocking density increased, whereas total yield of biomass was higher in the APH system (4.45 kg m-3 vs. 6.88 kg m-3). A low mortality (3% on average) was observed in both AP treatments. Overall, the results showed that a low initial stocking density at 2.5 kg m-3 improved the production of European Carp and of leafy vegetables by maintaining a better water quality in the tested AP system

Evaluation of Crop Insurance Yield Guarantees and Producer Welfare with Upward Trending Yields

Actual Production History (APH) yields play a critical role in determining the coverage offered to producers by the Risk Management Agency’s (RMA) Yield Protection, Revenue Protection, and Revenue Protection-Harvest Price Exclusion crop insurance products. The RMA currently uses the simple average of from 4 to 10 years of historical yields to determine the APH yield guarantee. If crop yields are trending upward, use of a simple average of historical yields introduces bias into the insurance offering. Using both county and individual insured unit data, we examine the producer impact of APH yield trends for Texas cotton and Illinois corn. Our findings indicate that biases due to using simple average APH yields when yields are trending upward reduce the expected indemnity and actuarially fair premium rate. Certainty equivalent differences are computed and used as a measure of the magnitude of welfare effect of trend-based biases in APH yields. The estimated welfare effect also varies significantly with different commonly used detrending approaches. This study demonstrates that producer welfare can be enhanced through proper treatment of yield trends in crop insurance programs.Actual Production History, Crop Insurance, Yield Trend, Yield Guarantee, Production Economics, Risk and Uncertainty,

Aphids associated with shrubs, herbaceous plants and crops in the Maltese Archipelago (Hemiptera, Aphidoidea)

A survey of the aphids associated with Maltese shrubs, herbaceous plants and crops was carried out. Sixty six aphid species were recorded from more than 90 species of host plants. Forty eight aphids were recorded from the Maltese islands for the fi rst time bringing the total number of aphid species known from these islands to 99. New records include: Acyrthosiphon lactucae, A. pisum, Anoecia vagans, Aphis alienus, A. euphorbiae, A. hederae, A. lambersi, A. multifl orae, A. nasturtii, A. parietariae, A. picridicola, A. ruborum, A. sedi, Aulacorthum solani, Brachycaudus helichrysi, Capitophorus sp. nr. similis, Clypeoaphis suaedae, Cryptomyzus korschelti, Dysaphis apiifolia, D. foeniculus, D. pyri, D. tulipae, Hyadaphis coriandri, H. foeniculi, H. passerinii, Hyperomyzus lactucae, Idiopterus nephrelepidis, Macrosiphoniella absinthii, M. artemisiae, M. sanborni, Macrosiphum euphorbiae, Ma. rosae, Melanaphis donacis, Metopolophium dirhodum, Pterochloroides persicae, Rectinasus buxtoni, Rhopalosiphum maidis, R. padi, R. rufi abdominale, Schizaphis graminum, Semiaphis dauci, Sipha maydis, Sitobion avenae, S. fragariae, Therioaphis alatina, Uroleucon inulae, U. hypochoeridis and U. sonchi. Of these 99 aphid species, 58 are of economic importance and 16 are alien introductions. For 15 of the aphid species, a total of 22 new host-plant records are made. Ten species of ants were found attending 18 aphid species.peer-reviewe

Light Absorption by Suspended Particles in the Red Sea: Effect of Phytoplankton Community Size Structure and Pigment Composition

The light absorption properties of phytoplankton (aph(λ)) and non-algal particles (anap(λ)) associated with phytoplankton pigments were analyzed across the Red Sea, in the upper 200 m depth, between October 2014 and August 2016. The contribution by non-algal particles to the total particulate light absorption (aph(λ)+ anap(λ)) was highly variable (23 ± 17% at 440 nm) and no relationship between anap(440) and chlorophyll a concentration, [TChl a], was observed. Phytoplankton specific phytoplankton absorption coefficients at 440 and 676 nm for a given [TChl a], aph*(440) and aph*(676), were slightly higher than those derived from average relationships for open ocean waters within the surface layer as well as along the water column. Variations in the concentration of photosynthetic and photoprotective pigments were noticeable by changes in phytoplankton community size structure as well as in aph*(λ). This study revealed that a higher proportion of picophytoplankton and an increase in photoprotective pigments (mainly driven by zeaxanthin) tended to be responsible for the higher aph*(λ) values found in the Red Sea as compared to other oligotrophic regions with similar [TChl a]. Understanding this variability across the Red Sea may help improve the accuracy of biogeochemical parameters, such as [TChl a], derived from in situ measurements and ocean color remote sensing at a regional scale

Assembly, trafficking and function of gamma-secretase

gamma-Secretase catalyzes the final cleavage of the beta-amyloid precursor protein to generate amyloid-beta peptide, the principal component of amyloid plaques in the brains of patients suffering from Alzheimer's disease. Here, we review the identification of gamma-secretase as a protease complex and its assembly and trafficking to its site(s) of cellular function. In reconstitution experiments, gamma-secretase was found to be composed of four integral membrane proteins, presenilin (PS), nicastrin (NCT), PEN-2 and APH-1 that are essential and sufficient for gamma-secretase activity. PS, which serves as a catalytic subunit of gamma-secretase, was identified as a prototypic member of novel aspartyl proteases of the GxGD type. In human cells, gamma-secretase could be further defined as a heterogeneous activity consisting of distinct complexes that are composed of PS1 or PS2 and APH-1a or APH-1b homologues together with NCT and PEN-2. Using green fluorescent protein as a reporter we localized PS and gamma-secretase activity at the plasma membrane and endosomes. Investigation of gamma-secretase complex assembly in knockdown and knockout cells of the individual subunits allowed us to develop a model of complex assembly in which NCT and APH-1 first stabilize PS before PEN-2 assembles as the last component. Furthermore, we could map domains in PS and PEN-2 that govern assembly and trafficking of the complex. Finally, Rer1 was identified as a PEN-2-binding protein that serves a role as an auxiliary factor for gamma-secretase complex assembly. Copyright (c) 2006 S. Karger AG, Basel