Effect of compaction on microbial activity and carbon and nitrogen transformations in two oxisols with different mineralogy

The use of machinery in agricultural and forest management activities frequently increases soil compaction, resulting in greater soil density and microporosity, which in turn reduces hydraulic conductivity and O2 and CO2 diffusion rates, among other negative effects. Thus, soil compaction has the potential to affect soil microbial activity and the processes involved in organic matter decomposition and nutrient cycling. This study was carried out under controlled conditions to evaluate the effect of soil compaction on microbial activity and carbon (C) and nitrogen (N) mineralization. Two Oxisols with different mineralogy were utilized: a clayey oxidic-gibbsitic Typic Acrustox and a clayey kaolinitic Xantic Haplustox (Latossolo Vermelho-Amarelo ácrico - LVA, and Latossolo Amarelo distrófico - LA, respectively, in the Brazil Soil Classification System). Eight treatments (compaction levels) were assessed for each soil type in a complete block design, with six repetitions. The experimental unit consisted of PVC rings (height 6 cm, internal diameter 4.55 cm, volume 97.6 cm³). The PVC rings were filled with enough soil mass to reach a final density of 1.05 and 1.10 kg dm-3, respectively, in the LVA and LA. Then the soil samples were wetted (0.20 kg kg-1 = 80 % of field capacity) and compacted by a hydraulic press at pressures of 0, 60, 120, 240, 360, 540, 720 and 900 kPa. After soil compression the new bulk density was calculated according to the new volume occupied by the soil. Subsequently each PVC ring was placed within a 1 L plastic pot which was then tightly closed. The soils were incubated under aerobic conditions for 35 days and the basal respiration rate (CO2-C production) was estimated in the last two weeks. After the incubation period, the following soil chemical and microbiological properties were detremined: soil microbial biomass C (C MIC), total soil organic C (TOC), total N, and mineral N (NH4+-N and NO3--N). After that, mineral N, organic N and the rate of net N mineralization was calculated. Soil compaction increased NH4+-N and net N mineralization in both, LVA and LA, and NO3--N in the LVA; diminished the rate of TOC loss in both soils and the concentration of NO3--N in the LA and CO2-C in the LVA. It also decreased the C MIC at higher compaction levels in the LA. Thus, soil compaction decreases the TOC turnover probably due to increased physical protection of soil organic matter and lower aerobic microbial activity. Therefore, it is possible to conclude that under controlled conditions, the oxidic-gibbsitic Oxisol (LVA) was more susceptible to the effects of high compaction than the kaolinitic (LA) as far as organic matter cycling is concerned; and compaction pressures above 540 kPa reduced the total and organic nitrogen in the kaolinitic soil (LA), which was attributed to gaseous N losses.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Diagnostic and ethical challenges in disorders of consciousness and locked-in syndrome: a survey of German neurologists.

Diagnosis and decisions on life-sustaining treatment (LST) in disorders of consciousness, such as the vegetative state (VS) and the minimally conscious state (MCS), are challenging for neurologists. The locked-in syndrome (LiS) is sometimes confounded with these disorders by less experienced physicians. We aimed to investigate (1) the application of diagnostic knowledge, (2) attitudes concerning limitations of LST, and (3) further challenging aspects in the care of patients. A vignette-based online survey with a randomized presentation of a VS, MCS, or LiS case scenario was conducted among members of the German Society for Neurology. A sample of 503 neurologists participated (response rate 16.4%). An accurate diagnosis was given by 86% of the participants. The LiS case was diagnosed more accurately (94%) than the VS case (79%) and the MCS case (87%, p < 0.001). Limiting LST for the patient was considered by 92, 91, and 84% of the participants who accurately diagnosed the VS, LiS, and MCS case (p = 0.09). Overall, most participants agreed with limiting cardiopulmonary resuscitation; a minority considered limiting artificial nutrition and hydration. Neurologists regarded the estimation of the prognosis and determination of the patients' wishes as most challenging. The majority of German neurologists accurately applied the diagnostic categories VS, MCS, and LiS to case vignettes. Their attitudes were mostly in favor of limiting life-sustaining treatment and slightly differed for MCS as compared to VS and LiS. Attitudes toward LST strongly differed according to circumstances (e.g., patient's will opposed treatment) and treatment measures.

Therapeutic drug monitoring of seven psychotropic drugs and four metabolites in human plasma by HPLC-MS.

A simple and sensitive LC-MS method was developed and validated for the simultaneous quantification of aripiprazole (ARI), atomoxetine (ATO), duloxetine (DUL), clozapine (CLO), olanzapine (OLA), sertindole (STN), venlafaxine (VEN) and their active metabolites dehydroaripiprazole (DARI), norclozapine (NCLO), dehydrosertindole (DSTN) and O-desmethylvenlafaxine (OVEN) in human plasma. The above mentioned compounds and the internal standard (remoxipride) were extracted from 0.5 mL plasma by solid-phase extraction (mix mode support). The analytical separation was carried out on a reverse phase liquid chromatography at basic pH (pH 8.1) in gradient mode. All analytes were monitored by MS detection in the single ion monitoring mode and the method was validated covering the corresponding therapeutic range: 2-200 ng/mL for DUL, OLA, and STN, 4-200 ng/mL for DSTN, 5-1000 ng/mL for ARI, DARI and finally 2-1000 ng/mL for ATO, CLO, NCLO, VEN, OVEN. For all investigated compounds, good performance in terms of recoveries, selectivity, stability, repeatability, intermediate precision, trueness and accuracy, was obtained. Real patient plasma samples were then successfully analysed.

Agglomeration and labour productivity in Spanish industry: a long-term analysis

This paper analyzes the relationship between spatial density of economic activity and interregional differences in the productivity of industrial labour in Spain during the period 1860-1999. In the spirit of Ciccone and Hall (1996) and Ciccone (2002), we analyze the evolution of this relationship over the long term in Spain. Using data on the period 1860-1999 we show the existence of an agglomeration effect linking the density of economic activity with labour productivity in the industry. This effect was present since the beginning of the industrialization process in the middle of the 19th century but has been decreasing over time. The estimated elasticity of labour productivity with respect to employment density was close to 8% in the subperiod 1860-1900, reduces to a value of around 7% in the subperiod 1914-1930, to 4% in the subperiod 1965-1979 and becomes insignificant in the final subperiod 1985-1999. At the end of the period analyzed there is no evidence of the existence of net agglomeration effects in the industry. This result could be explained by an important increase in the congestion effects in large industrial metropolitan areas that would have compensated the centripetal or agglomeration forces at work. Furthermore, this result is also consistent with the evidence of a dispersion of industrial activity in Spain during the last decades.

Simultaneous determination of Pu and Am radioisotopes in environmental samples: a tool for determining origin and release date

A radiochemical procedure was developed for the sequential determination of Pu and Am radioisotopes in environmental samples. The radioisotope activities were then used to assess the origin and release date of the environmental plutonium. The radioanalytical procedure is based on the separation of Pu and Am on selective extraction chromatographic resins (Eichrom TEVA and DGA). Alpha sources were prepared by electrodeposition on stainless steel discs, and the alpha emitting radionuclides (238Pu, 239,240Pu and 241Am) were measured by alpha spectrometry. For the determination of the beta emitting 241Pu, the Pu alpha source was leached in hot concentrated nitric acid and the Pu fraction further purified by extraction chromatography on a small column of TEVA resin (100 μg of resin in a pipette tip). 241Pu is then measured by ultra low level liquid scintillation counting. Due to the lack of reference material for 241Pu, the proposed radiochemical method was nevertheless validated using four IAEA reference sediments with information values of 241Pu. The proposed method was then used to determine the 238Pu, 239,240Pu, 241Pu and 241Am activity concentrations in alpine soils of France and Switzerland. The soil is the primary receptor of the atmospheric radioactive fallout and, because of the strong binding interaction with soils particles, the isotopes are little fractionated. Therefore, the activity ratios 241Pu/239+240Pu and 238Pu/239,240Pu in soil samples were used to determine the origin (source) and date of the Pu contamination in the investigated alpine sites. The 241Pu/239,240Pu and 238Pu/239,240Pu activity ratios confirmed that the main origin of Pu in the alpine soils was the global fallout from the nuclear bomb tests (NBT) in the fifties and sixties. Furthermore, the 241Pu/241Am activity ratios were used to determine the age of the Pu contamination, which is also an important data for distinguishing the Pu sources. The estimation of the date of the contamination, by the 241Pu/241Am age-dating method, further confirmed the NBT as the Pu source. However, the 241Pu/241Am dating method was limited to samples where Pu-Am fractionation was insignificant. If any, the contribution of the Chernobyl accident in the studied sites is negligible.

Sequential decisions in allocation problems

[eng] In the context of cooperative TU-games, and given an order of players, we consider the problem of distributing the worth of the grand coalition as a sequentia decision problem. In each step of process, upper and lower bounds for the payoff of the players are required related to successive reduced games. Sequentially compatible payoffs are defined as those allocation vectors that meet these recursive bounds. The core of the game is reinterpreted as a set of sequentally compatible payoffs when the Davis-Maschler reduced game is considered (Th.1). Independently of the reduction, the core turns out to be the intersections of the family of the sets of sequentially compatible payoffs corresponding to the different possible orderings (Th.2), so it is in some sense order-independent. Finally, we analyze advantagenous properties for the first player

An Essential Role for Insulin and IGF1 Receptors in Regulating Sertoli Cell Proliferation, Testis Size, and FSH Action in Mice.

Testis size and sperm production are directly correlated to the total number of adult Sertoli cells (SCs). Although the establishment of an adequate number of SCs is crucial for future male fertility, the identification and characterization of the factors regulating SC survival, proliferation, and maturation remain incomplete. To investigate whether the IGF system is required for germ cell (GC) and SC development and function, we inactivated the insulin receptor (Insr), the IGF1 receptor (Igf1r), or both receptors specifically in the GC lineage or in SCs. Whereas ablation of insulin/IGF signaling appears dispensable for GCs and spermatogenesis, adult testes of mice lacking both Insr and Igf1r in SCs (SC-Insr;Igf1r) displayed a 75% reduction in testis size and daily sperm production as a result of a reduced proliferation rate of immature SCs during the late fetal and early neonatal testicular period. In addition, in vivo analyses revealed that FSH requires the insulin/IGF signaling pathway to mediate its proliferative effects on immature SCs. Collectively, these results emphasize the essential role played by growth factors of the insulin family in regulating the final number of SCs, testis size, and daily sperm output. They also indicate that the insulin/IGF signaling pathway is required for FSH-mediated SC proliferation.

Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts.

The function of DNA-binding proteins is controlled not just by their abundance, but mainly at the level of their activity in terms of their interactions with DNA and protein targets. Moreover, the affinity of such transcription factors to their target sequences is often controlled by co-factors and/or modifications that are not easily assessed from biological samples. Here, we describe a scalable method for monitoring protein-DNA interactions on a microarray surface. This approach was designed to determine the DNA-binding activity of proteins in crude cell extracts, complementing conventional expression profiling arrays. Enzymatic labeling of DNA enables direct normalization of the protein binding to the microarray, allowing the estimation of relative binding affinities. Using DNA sequences covering a range of affinities, we show that the new microarray-based method yields binding strength estimates similar to low-throughput gel mobility-shift assays. The microarray is also of high sensitivity, as it allows the detection of a rare DNA-binding protein from breast cancer cells, the human tumor suppressor AP-2. This approach thus mediates precise and robust assessment of the activity of DNA-binding proteins and takes present DNA-binding assays to a high throughput level.

Plants and tortoises: mutations in the Arabidopsis jasmonate pathway increase feeding in a vertebrate herbivore.

Photosynthetic tissues, the major food source of many invertebrates and vertebrates, are well defended. Many defence traits in leaves are controlled via the jasmonate signalling pathway in which jasmonate acts as a hormone by binding to a receptor to activate responses that lead to increased resistance to invertebrate folivores. We predicted that mutations in jasmonate synthesis might also increase the vulnerability of leaves to vertebrate folivores and tested this hypothesis using the Eastern Hermann's tortoise (Eurotestudo boettgeri) and an Arabidopsis thaliana (Brassicaceae) allene oxide synthase (aos) mutant unable to synthesize jasmonate. Tortoises preferred the aos mutant over the wild type (WT). Based on these results, we then investigated the effect of mutating jasmonate perception using a segregating population of the recessive A. thaliana jasmonate receptor mutant coronatine insensitive1-1 (coi1-1). Genotyping of these plants after tortoise feeding revealed that the homozygous coi1-1 receptor mutant was consumed more readily than the heterozygous mutant or the WT. Therefore, the plant's ability to synthesize or perceive jasmonate reduces feeding by a vertebrate herbivore. We also tested whether or not tortoise feeding behaviour was influenced by glucosinolates, the principal defence chemicals in Arabidopsis leaves with known roles in defence against many generalist insects. However, in contrast to what has been observed with such insects, leaves in which the levels of these compounds were reduced genetically were consumed at a similar rate to those of the WT.

Agglomeration and labour productivity in Spanish industry: a long-term analysis

This paper analyzes the relationship between spatial density of economic activity and interregional differences in the productivity of industrial labour in Spain during the period 1860-1999. In the spirit of Ciccone and Hall (1996) and Ciccone (2002), we analyze the evolution of this relationship over the long term in Spain. Using data on the period 1860-1999 we show the existence of an agglomeration effect linking the density of economic activity with labour productivity in the industry. This effect was present since the beginning of the industrialization process in the middle of the 19th century but has been decreasing over time. The estimated elasticity of labour productivity with respect to employment density was close to 8% in the subperiod 1860-1900, reduces to a value of around 7% in the subperiod 1914-1930, to 4% in the subperiod 1965-1979 and becomes insignificant in the final subperiod 1985-1999. At the end of the period analyzed there is no evidence of the existence of net agglomeration effects in the industry. This result could be explained by an important increase in the congestion effects in large industrial metropolitan areas that would have compensated the centripetal or agglomeration forces at work. Furthermore, this result is also consistent with the evidence of a dispersion of industrial activity in Spain during the last decades.

Differences in low-grade chronic inflammation and insulin resistance in women with previous gestational diabetes mellitus and women with polycystic ovary syndrome.

BACKGROUND: Polycystic ovary syndrome (PCOS) and gestational diabetes mellitus (GDM) are both characterized by an increase in insulin resistance. Our goal in the present study was to measure insulin resistance (as estimated by homeostasis model assessment, sex hormone-binding globulin (SHBG) and adiponectin concentrations) and parameters of low-grade inflammation in non-diabetic, non-hyperandrogenic ovulatory women with previous GDM (pGDM) and in non-diabetic women with classic PCOS, characterized by hyperandrogenism and oligo/anovulation. PATIENTS AND DESIGN: We evaluated 20 women with PCOS, 18 women with pGDM and 19 controls, all matched according to body mass index (BMI). Fasting blood samples were drawn in all women 3-6 days after spontaneous or dydrogesterone-induced withdrawal bleeding. Body fat distribution was assessed using dual-energy X-ray absorptiometry in all women. RESULTS: After adjusting for age and percent body fat, measures of insulin resistance such as SHBG and adiponectin concentrations were decreased and central obesity was increased in women with PCOS and pGDM compared with controls (all p < 0.05). Parameters of low-grade inflammation such as serum tumor necrosis factor-alpha and highly sensitive C-reactive protein concentrations, white blood cell and neutrophil count were increased only in women with PCOS compared with BMI-matched controls (all p < 0.05). CONCLUSIONS: Certain markers of insulin resistance are increased in both women with PCOS and women with pGDM, while low-grade inflammation is increased only in PCOS. PCOS and GDM might represent specific phenotypes of one disease entity with an increased risk of cardiovascular disease, whereby women with PCOS demonstrate an augmented cardiovascular risk profile.

Behavioural types and ecological effects in a natural population of the cooperative cichlid Neolamprologus pulcher

The ecological relevance of behavioural syndromes is little studied in cooperative breeding systems where it is assumed that the behavioural type might influence individual decisions on helping and dispersal (e.g. shy, nonaggressive and nonexplorative individuals remain philopatric and helpful, whereas bold, aggressive, explorative individuals compete for vacancies outside their group and disperse). We measured the behavioural type of 19 subordinates in the cooperatively breeding cichlid fish Neolamprologus pulcher in their natural environment by quantifying six behavioural traits up to four times ('trials') in three different contexts, by presenting them with a conspecific intruder, a predator or nothing inside a tube. We found only moderate within-context repeatability (intraclass correlation coefficients) of the focal individual's behaviour, except for attacking either the conspecific or the predator inside the tube. The focal individual's attack rate of the tube was also positively affected by its group size. Averaging traits per context removed the between-trial variation, and consequently the across-context repeatability was very high for all six traits, except for territory maintenance. Trait values depended significantly on the context, except for territory defence. Consequently, individuals could be classified into different behavioural types based on their reaction towards the tube, but surprisingly, and opposite to laboratory studies in this species, ranging propensity and territory maintenance were not included in this behavioural syndrome. We suggest that more studies are needed to compare standardized focal personality tests (e.g. exploration propensity) with actual behaviour observed in nature (e.g. ranging and dispersal).

Detecting and measuring deprivation in primary care: development, validity and reliability of a self-reported questionnaire - the DiPCare-Q

Background: General practitioners play a central role in taking deprivation into consideration when caring for patients in primary care. Validated questions to identify deprivation in primary-care practices are still lacking. For both clinical and research purposes, this study therefore aims to develop and validate a standardized instrument measuring both material and social deprivation at an individual level. Methods: The Deprivation in Primary Care Questionnaire (DiPCare-Q) was developed using qualitative and quantitative approaches between 2008 and 2011. A systematic review identified 199 questions related to deprivation. Using judgmental item quality, these were reduced to 38 questions. Two focus groups (primary-care physicians, and primary-care researchers), structured interviews (10 laymen), and think aloud interviews (eight cleaning staff) assured face validity. Item response theory analysis was then used to derive the DiPCare-Q index using data obtained from a random sample of 200 patients who were to complete the questionnaire a second time over the phone. For construct and criterion validity, the final 16 questions were administered to a random sample of 1,898 patients attending one of 47 different private primary-care practices in western Switzerland (validation set) along with questions on subjective social status (subjective SES ladder), education, source of income, welfare status, and subjective poverty. Results: Deprivation was defined in three distinct dimensions (table); material deprivation (eight items), social deprivation (five items) and health deprivation (three items). Item consistency was high in both the derivation (KR20 = 0.827) and the validation set (KR20 = 0.778). The DiPCare-Q index was reliable (ICC = 0.847). For construct validity, we showed the DiPCare-Q index to be correlated to patients' estimation of their position on the subjective SES ladder (rs = 0.539). This position was correlated to both material and social deprivation independently suggesting two separate mechanisms enhancing the feeling of deprivation. Conclusion: The DiPCare-Q is a rapid, reliable and validated instrument useful for measuring both material and social deprivation in primary care. Questions from the DiPCare-Q are easy to use when investigating patients' social history and could improve clinicians' ability to detect underlying social distress related to deprivation.

A new aggregation method for strategic decision making and its application in assignment theory

A new aggregation method for decision making is presented by using induced aggregation operators and the index of maximum and minimum level. Its main advantage is that it can assess complex reordering processes in the aggregation that represent complex attitudinal characters of the decision maker such as psychological or personal factors. A wide range of properties and particular cases of this new approach are studied. A further generalization by using hybrid averages and immediate weights is also presented. The key issue in this approach against the previous model is that we can use the weighted average and the ordered weighted average in the same formulation. Thus, we are able to consider the subjective attitude and the degree of optimism of the decision maker in the decision process. The paper ends with an application in a decision making problem based on the use of the assignment theory.