Stable C and N isotope variation during anaerobic digestate composting and in the compost-amended soil-plant system.

Although the use of composts derived from anaerobic digestates as soil amendments is likely to increase in the future, there is little information concerning the fate of their C and N compounds after their incorporation into soil. This work assesses C and N concentrations and the associated changes in δ15N and δ13C during the composting processes of cattle and pig slurry anaerobic digestates. In addition, the compost effect on C and N fractions and plant uptake were studied during a six-month pot experiment with rosemary plants. The results did not show δ13C and δ15N isotopic discrimination during composting, indicating a previous stabilization of cattle manure and pig slurry during the anaerobic digestion. This fact was also confirmed by the low C losses during the composting processes (1.2-fold and 1.05-fold for the composting piles with cattle and pig slurry anaerobic digestates, respectively). After soil addition, the composts augmented N values (from 0.41 g kg-1 to around 0.56 g kg-1 in low dose and 0.68 g kg-1 in high dose compost amended soils) and δ15N soil values (increases in the range of 50%-156%), but showed only slight differences in C and δ13C values compared to unfertilised control and inorganic fertilized soils. Moreover, the rosemary leaves of the plants grown on the compost amended soils presented higher N and δ15N abundance than control and inorganic fertilized plants. We conclude that δ15N abundance of anaerobic digestate composts is useful to discern its N uptake and could thus be a useful tool to detect whether organic or mineral fertiliser types were used for agricultural production.

Towards a global-scale soil climate mitigation strategy.

Sustainable soil carbon sequestration practices need to be rapidly scaled up and implemented to contribute to climate change mitigation. We highlight that the major potential for carbon sequestration is in cropland soils, especially those with large yield gaps and/or large historic soil organic carbon losses. The implementation of soil carbon sequestration measures requires a diverse set of options, each adapted to local soil conditions and management opportunities, and accounting for site-specific trade-offs. We propose the establishment of a soil information system containing localised information on soil group, degradation status, crop yield gap, and the associated carbon-sequestration potentials, as well as the provision of incentives and policies to translate management options into region- and soil-specific practices.

Adding worms during composting of organic waste with red mud and fly ash reduces CO2 emissions and increases plant available nutrient contents.

Alkaline industrial wastes such as red mud and fly ash are produced in large quantities. They may be recycled as bulking agent during composting and vermicomposting, converting organic waste into soil amendments or plant growth media. The aim of this study was to assess the microbial parameters, greenhouse gas emissions and nutrient availability during composting and vermicomposting of household waste with red mud and fly ash 15% (dry weight). CO2, CH4 and N2O emissions were monitored during 6 months in controlled laboratory conditions and microbial biomass and phospholipid acids, N and P availability were analysed in the end-products. Higher CO2 emissions were observed during vermicomposting compared to composting. These emissions were decreased by red mud addition, while fly ash had no effect. Nitrate (NO3-N) content of the end-products were more affected by worms than by alkaline materials, while higher ammonium (NH4-N) contents were recorded for composts than vermicomposts. Red mud vermicompost showed higher soluble P proportion than red mud compost, suggesting that worm presence can counterbalance P adsorption to the inorganic matrix. Final composts produced with red mud showed no harmful heavy metal concentrations. Adding worms during composting thus improved the product nutrient availability and did not increase metal toxicity. From a practical point of view, this study suggests that for carbon stabilisation and end-product quality, the addition of red mud during composting should be accompanied by worm addition to counterbalance negative effects on nutrient availability.

Does grassland introduction into cropping cycles affect carbon dynamics through changes of allocation of soil organic matter within aggregate fractions?

Implementation of ley grassland into crop rotation could have positive influence in soil ecosystem services such as C storage. The periodical changes of land-use plus the in situ labelling given by the introduction of maize crops under ley grassland induce differences in soil organic matter (SOM) that could be traced either by stable isotopes or by the characterization of plant biomarkers such as lignin derived phenols. Evaluation of SOM dynamics is often limited by the complexity of soil matrix. To override these limitations, a hierarchical approach to decompose the soil mosaic into aggregates has been proposed in this study. Soil and plant samples were collected from a long-term experimental area in Lusignan (western France). Soils from four different treatments (bare fallow, permanent maize, permanent grassland, and ley grassland based on 6years of grassland followed by 3years of maize) were sampled, fractionated into water stable aggregates, and finally analysed for carbon, nitrogen, and lignin contents, as well as for 13C isotopic signature. Soils under ley and permanent grassland stored higher amount of SOM in larger aggregates and preserved more efficiently the lignin stocks than the corresponding samples under permanent maize. Contemporary, finer fraction of ley grassland showed higher mean residence time of organic carbon, probably due to a legacy effect of the previous years under grassland. Even if maize derived SOM was identified, the grassland footprint was still dominating the ley grassland soils, as described by the principal component analysis. Strong correlation between these results and the quality and stoichiometry of the vegetal litter returned to soil were found, evidencing the needs for a comprehensive evaluation at a molecular level of all the parameters modified by land-use changes, including tillage, to understand the potential for carbon storage of different agroecosystems.

Integrated genomic analysis of colorectal cancer progression reveals activation of EGFR through demethylation of the EREG promoter.

Key molecular drivers that underlie transformation of colonic epithelium into colorectal adenocarcinoma (CRC) are well described. However, the mechanisms through which clinically targeted pathways are activated during CRC progression have yet to be elucidated. Here, we used an integrative genomics approach to examine CRC progression. We used laser capture microdissection to isolate colonic crypt cells, differentiated surface epithelium, adenomas, carcinomas and metastases, and used gene expression profiling to identify pathways that were differentially expressed between the different cell types. We identified a number of potentially important transcriptional changes in developmental and oncogenic pathways, and noted a marked upregulation of EREG in primary and metastatic cancer cells. We confirmed this pattern of gene expression by in situ hybridization and observed staining consistent with autocrine expression in the tumor cells. Upregulation of EREG during the adenoma-carcinoma transition was associated with demethylation of two key sites within its promoter, and this was accompanied by an increase in the levels of epidermal growth factor receptor (EGFR) phosphorylation, as assessed by reverse-phase protein analysis. In CRC cell lines, we demonstrated that EREG demethylation led to its transcriptional upregulation, higher levels of EGFR phosphorylation, and sensitization to EGFR inhibitors. Low levels of EREG methylation in patients who received cetuximab as part of a phase II study were associated with high expression of the ligand and a favorable response to therapy. Conversely, high levels of promoter methylation and low levels of EREG expression were observed in tumors that progressed after treatment. We also noted an inverse correlation between EREG methylation and expression levels in several other cancers, including those of the head and neck, lung and bladder. Therefore, we propose that upregulation of EREG expression through promoter demethylation might be an important means of activating the EGFR pathway during the genesis of CRC and potentially other cancers.

Nature and decomposition degree of cover crops influence pesticide sorption: quantification and modelling.

This study quantifies and models the influence of the type and the degree of decomposition of cover crops (CC) on three pesticides sorption: epoxiconazole (EPX), S-metolachlor (SMOC) and glyphosate (GLY). Residues of four cover crop species were incubated for 0, 6, 28 or 56 d in controlled conditions. For each incubation time, adsorption of pesticides on CC residues was measured in batch experiments. Additionally, the biochemical and elemental composition (Van Soest fractionation, C:N, (13)C NMR spectroscopy) of CC was characterized. Mineralization of CC residues was monitored at all incubation times using CO2 trapping. Results showed that the adsorption of pesticides differed significantly according to (i) the type of molecule, (ii) the type of CC, (iii) the degree of CC decomposition and the interaction CC×decomposition time. EPX and GLY were the most (Kd ranging from 188 to 267 L kg(-1)) and the least (Kd ranging from 18 to 28 L kg(-1)) sorbed pesticides respectively. With increasing decomposition of the CC residue, sorption increased by 1.6- to 4.7-fold according to the type of pesticide and cover crop. It was significantly correlated with the net cumulative mineralization (ρ>0.7) and other indicators of biochemical composition such as C:N ratio (ρ<-0.7), the Van Soest neutral detergent soluble fraction (ρ>0.5) and the alkyl/O-alkyl C ratio determined by NMR. An innovative model based on net cumulative mineralization of CC residues is proposed to describe the pesticide sorption and appears to be a promising approach to account for the effects of decaying plant residues on the environmental fate of pesticides.

The effects of frozen tissue storage conditions on the integrity of RNA and protein.

Unfixed tissue specimens most frequently are stored for long term research uses at either -80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5-12 years at -80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for -80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at -80° C compared to those stored in VPLN. Long term storage of human research tissues at -80° C provides at least the same quality of RNA and protein as storage in VPLN.

Chemical composition of organic matter in extremely acid, lignite-containing lake sediments impacted by fly ash contamination.

In the Lusatian lignite mining district of eastern Germany, extremely acid lakes developed during ground water rising after exploitation of lignite in open-cast mines. The reasons of plant colonization (Juncus bulbosus L.) of some lakes exhibiting moderate pH values while others remain extremely acid and unvegetated are unknown. Alkalinity gain may be achieved by addition of alkaline materials and/or decomposition of organic matter. Our objective was to examine fly ash deposition and the resulting changes in organic matter composition in the uppermost 0 to 5 cm of the sediment sampled from vegetated and unvegetated lakes. Bulk soil and particle size fractions were analyzed for elemental composition, magnetic susceptibility, and chemical structure of the organic matter by 13C solid-state nuclear magnetic resonance (NMR) spectroscopy. The lignite content of the samples was estimated by 14C activity measurements. The pH values decreased with increasing depth and the changes in pH were found to be correlated with changes in magnetic susceptibility. Carbon and nitrogen contents were found to decrease with increasing depth. The C to N ratios are consistent with the (i) the presence of decomposing plant residues and/or microbial material such as algae in the upper 0 to 5 cm of the sediment and (ii) the dominance of lignite in the layers below this depth as confirmed by 14C activity measurements. The structural analyses of the particle size separates from the 0- to 5-cm depth were consistent with the presence of organic matter derived from plant material. This study confirms that fly ash is an important source of alkalinity in the upper 0 to 5 cm of the sediment that enhanced plant growth and led to enrichment of the sediment with organic matter derived from plant material.

Analysis of chromosome 9p21 deletion and p16 gene mutation in salivary gland carcinomas.

The chromosomal locus 9p21 contains the p16(INK4a/CDKN2/MTS1) tumor suppressor gene that has been implicated in a variety of tumor types, including carcinomas of the head and neck, esophagus, and pancreas. To determine whether the loss of this gene is involved in salivary gland cancers, 35 carcinomas and paired nonneoplastic specimens were analyzed for loss of heterozygosity (LOH) of polymorphic genetic markers located in the region of interest. Five types of salivary gland tumors were studied: mucoepidermoid carcinoma, salivary duct carcinoma, adenoid cystic carcinoma, acinic cell carcinoma, and polymorphous low-grade adenocarcinoma. Seven of 9 salivary duct carcinomas showed LOH of 1 or more polymorphic markers. In 1 case of salivary duct carcinoma with LOH, we confirmed a deletion of bp 240-254 within exon 2. In addition, another salivary duct carcinoma showed a homozygous deletion of p16 in differential polymerase chain reaction analysis. Loss of heterozygosity was found in 1 of 10 adenoid cystic carcinomas and 1 of 8 mucoepidermoid carcinomas and was absent in the remaining subtypes. No mutations in exon 1 or exon 2 or homozygous deletion of p16 were found in these 2 particular neoplasms with LOH. These results suggest that inactivation of p16 is important in the development or progression of at least some salivary duct carcinomas, but we found no evidence that its alteration plays a role in the other subtypes examined.

Mapping of genetic deletions on the long arm of chromosome 4 in human esophageal adenocarcinomas.

Loss of the long arm of chromosome 4 has been identified previously as a common occurrence in adenocarcinomas of the esophagus and gastroesophageal junction by relatively low resolution genetic surveys. To better define the extent of 4q deletion in these neoplasms we isolated DNA from 29 primary carcinomas using microdissection, and used DNA obtained from xenografts of 14 carcinomas grown in immunodeficient mice in an assay of loss of heterozygosity of 25 polymorphic microsatellite markers distributed along the chromosomal arm. Two carcinomas exhibited widespread microsatellite instability and were excluded from deletion mapping. In the remaining 41 carcinomas, loss of heterozygosity was detected in 33 (80%). Twenty-three cancers showed complete or extensive reduction to homozygosity along the length of the long arm. Ten cancers had smaller discrete areas of loss and were principally useful in discerning three non-overlapping areas of consensus genetic deletion. Area 1 centered on marker D4S1534 at 4q21.1-22, area 2 centered on marker D4S620 at 4q32-33, and area 3 centered on marker D4S426 at 4q35. No known tumor suppressor genes map to these loci, but the frequent deletion of these areas in gastroesophageal carcinomas and in other carcinomas suggests that undiscovered tumor suppressor genes may reside here.

Mutations of c-kit JM domain are found in a minority of human gastrointestinal stromal tumors.

The c-kit gene encodes a transmembrane receptor kinase (KIT) which is expressed in the majority of human gastrointestinal stromal tumors (GISTs), a subtype of gastrointestinal mesenchymal neoplasms. A previous study identified mutations in the juxtamembrane (JM) domain of c-kit in five of six GISTs (Science 279: 577, 1998). To better define the frequency and spectrum of c-kit gene mutations in mesenchymal neoplasms of the GI tract that had been characterized for KIT protein expression, we examined archived tissue samples for mutations in the JM domain by PCR amplification and DNA sequencing. c-kit JM domain mutations were found in nine of 56 mesenchymal tumors (46 GISTs, eight leiomyomas, two leiomyosarcomas) and occurred exclusively in GISTs (21%). Seven of the nine mutations consisted of intragenic deletions of one to 19 codons. There was one insertion mutation that added 12 codons and one missense mutation (Val560Asp). None of the mutations disrupted the downstream reading frame of the gene. The single missense mutation (Val560Asp) is very similar to the only other missense mutation reported in GISTs (Val599Asp). Of the 46 GISTs, 43 were strongly positive for KIT protein expression and negative for diffuse expression of desmin. Neither KIT expression nor gene mutations were found in gastrointestinal leiomyomas or leiomyosarcomas. We conclude that mutation of the c-kit JM domain does not occur in gastrointestinal mesenchymal neoplasms with well developed-smooth muscle differentiation, and is restricted to GISTs. However, since these mutations are only found in a minority of GISTs, further investigation into the mechanisms of c-kit gene activation in this group of neoplasms is warranted.

Allelic deletion in 11p15 is a common occurrence in esophageal and gastric adenocarcinoma.

BACKGROUND: Esophageal adenocarcinoma and gastric adenocarcinoma have distinct epidemiologic characteristics, but they are morphologically identical and sometimes clinically indistinguishable. Recent work in molecular oncology suggests that cancer types have distinct molecular genetic profiles that may explain their biologic differences. Gastric adenocarcinoma has previously been shown to have a relatively high rate of deletion in chromosome 11. To determine whether similar genetic loci are involved in esophageal adenocarcinoma, we assayed for genetic loss in chromosome 11 in samples of these cancers. METHODS: Dissection of neoplastic and nonneoplastic tissue was performed under direct microscopic visualization from histologic sections of 15 gastric adenocarcinomas and 15 esophageal adenocarcinomas. After DNA extraction, polymerase chain amplification products of a series of polymorphic microsatellite markers on chromosome 11 were analyzed by polyacrylamide gel electrophoresis. Tumor specific chromosomal deletion was signaled by the loss of microsatellite alleles. RESULTS: A panel of 3 polymorphic markers in 11p15 revealed overall incidences of loss of heterozygosity (LOH) of 53.3% in esophageal adenocarcinomas and 61.5% in gastric adenocarcinomas. A panel of 3 polymorphic markers in 11q22-23.3 revealed overall incidences of LOH of 14.3% in esophageal adenocarcinomas and 31% in gastric adenocarcinomas. Diffuse microsatellite instability, which was consistent with a replication error phenotype, was found in 2 of 15 (13.3%) gastric adenocarcinomas but was not deleted in esophageal adenocarcinomas. CONCLUSIONS: Esophageal and gastric adenocarcinoma have a similar significant incidence of genetic loss in 11p15. This is suggestive of the presence of a tumor suppressor gene that may be inactivated in both tumor types.

The influence of weight on adolescent self-esteem.

Overweight children have traditionally been thought to have lower self-esteem than other children. Prospective data from the California Child Health and Development Studies were used to test this hypothesis by examination of the relationship between body mass index, self-esteem and locus of control while controlling for demographic and baseline psychosocial traits. Principle components and confirmatory factor analysis were used to derive latent constructs for self-esteem, locus of control and other psychosocial factors. A covariance structure model was developed using the results of the confirmatory factor analysis. In this model, adolescent self-esteem, locus of control and body mass index were not related. These findings from prospective data in a non-clinical population suggest that although some subgroups of obese children may be vulnerable for decreased self-esteem, this does not appear to be a significant problem in the general population.

Body mass index, weight change, and risk of mobility disability in middle-aged and older women. The epidemiologic follow-up study of NHANES I.

OBJECTIVE: As disability is highly prevalent among older women, is costly, and affects the quality of life, preventable causes of disability must be identified. In this study, we investigated the relationship between the body mass index (BMI), weight change, and the onset of disability in older women. DESIGN: Prospective cohort study. SETTING: The nationally representative US epidemiologic follow-up study of the National Health and Nutrition Examination Survey (NHANES) I (1971 through 1987). PATIENTS: White women classified as young-old (mean age 60 years at baseline, mean age 65 years at follow-up) and old-old (mean age 76 years at baseline, mean age 80 years at follow-up). MAIN OUTCOME MEASURES: The relative odds for the onset of mobility disability associated with tertiles of past BMI (measured 8 to 16 years prior to disability ascertainment) and current BMI (measured 2 to 5 years prior to disability ascertainment) and with weight change between the two weight measurements. RESULTS: In both cohorts, women in the high past BMI group (> 27 in the young-old and > 28.1 in the old-old cohort) had a twofold increase in the risk for disability compared with women in the low past BMI group. High current BMI was as strongly related as past BMI to risk of disability in the young-old women; it was not as strong a predictor in old-old women. In the old-old group only, women who experienced a weight loss of more than 5% had a twofold increase in risk of disability compared with weight-stable women. These results were adjusted for age, smoking, education, and study time and were not importantly modified with the addition into the models of single or multiple health conditions. CONCLUSIONS: These prospective data suggest that high BMI is a strong predictor of long-term risk for mobility disability in older women and that this risk persists even to very old age. However, the paradoxical increase in risk associated with weight loss in the old-old women requires further study. Programs to prevent overweight may have potential for decreasing disability in women.

The association between weight change and psychological well-being in women.

Previous studies on the effects of weight change on psychological well-being in clinical samples have yielded inconsistent results. We examined the relationship between weight change and psychological well-being as measured by the General Well-Being (GWB) scale in 3747 women aged 50 years or less at baseline using data from the NHANES I Epidemiologic Follow-up Study. Multiple logistic regression was used to estimate odds ratios while adjusting for potential confounders. Recent weight gain was associated with poorer well-being in both overweight and non-overweight women and recent weight loss with poorer well-being in non-overweight women. These findings were unchanged by controlling for age, race, marital status, employment status, education, physical activity level, number of medical conditions, alcohol use and extroversion. Thus, maintenance of stable weight may contribute to psychological well-being in women.

Modification of the relationship between the Quetelet index and mortality by weight-loss history among older women.

The effect of weight on mortality was examined using data from the first National Health and Nutrition Examination Survey (NHANES I) Epidemiologic Follow-up Study for white women aged 65 to 74 years at baseline. There was a U-shaped curve relating the Quetelet index categories to total mortality, with increased risk for both lean and heavy women. However, the increased risk to lean subjects occurred only among those who had lost more than 8.55% from their reported lifetime maximum weight. Controlling for baseline medical conditions, excluding early years of follow-up, and limiting the analysis to never-smokers did not greatly change the results. Lean women with stable weight have the lowest risk of mortality, while those who have lost weight have a high risk. Heavy women have a high risk of mortality regardless of weight-loss history. Thus, the effect of weight on mortality is modified by history of weight loss in older women, even when accounting for factors associated with weight loss and increased mortality risk.

Lyme disease in South Carolina.

Lyme disease is present in South Carolina, though not as prevalent as in many other states in the country. The characteristics of South Carolina cases are similar to those of the nation as a whole. The tick vector of Lyme disease in the Southeast is not clearly established, but is thought to be Ixodes scapularis. Questions remain concerning the prevalence of infection in local ticks with Borrelia burgdorferi, and the risk to a person bitten by a tick in South Carolina.

Taxonomy of the Lyme disease spirochetes.

Morphology, physiology, and DNA nucleotide composition of Lyme disease spirochetes, Borrelia, Treponema, and Leptospira were compared. Morphologically, Lyme disease spirochetes resemble Borrelia. They lack cytoplasmic tubules present in Treponema, and have more than one periplasmic flagellum per cell end and lack the tight coiling which are characteristic of Leptospira. Lyme disease spirochetes are also similar to Borrelia in being microaerophilic, catalase-negative bacteria. They utilize carbohydrates such as glucose as their major carbon and energy sources and produce lactic acid. Long-chain fatty acids are not degraded but are incorporated unaltered into cellular lipids. The diamino amino acid present in the peptidoglycan is ornithine. The mole % guanine plus cytosine values for Lyme disease spirochete DNA were 27.3-30.5 percent. These values are similar to the 28.0-30.5 percent for the Borrelia but differed from the values of 35.3-53 percent for Treponema and Leptospira. DNA reannealing studies demonstrated that Lyme disease spirochetes represent a new species of Borrelia, exhibiting a 31-59 percent DNA homology with the three species of North American borreliae. In addition, these studies showed that the three Lyme disease spirochetes comprise a single species with DNA homologies ranging from 76-100 percent. The three North American borreliae also constitute a single species, displaying DNA homologies of 75-95 percent. Lyme disease spirochetes and Borrelia exhibited little or no DNA homology (0-2 percent) with the Treponema or Leptospira. Plasmids were present in the three Lyme disease spirochetes and the three North American borreliae.