Aluminum hydroxy-interlayered minerals and chemical properties of a subtropical Brazilian Oxisol under no-tillage and conventional tillage

No tillage systems significantly influence the soil system, but knowledge about the effects on the mineralogy of tropical and subtropical soils is limited. This study evaluated the long-term effects (26 years) of no-tillage (NT) on aluminum hydroxy-interlayered minerals of a subtropical Oxisol in Southern Brazil (Guarapuava, PR), compared to the same soil under conventional tillage (CT). The clay fraction (< 2 µm) in soil samples of the surface horizons of a field experiment under both management systems was analyzed by X-ray diffraction (XRD) to identify and characterize Al hydroxy-interlayered minerals before and after treatment with sodium citrate to remove intra-layer material. Soil liquid (solution) and solid phases were also characterized. The contents of total organic C, exchangeable cations, P, and the values of extractable acidity and cation exchange capacity as well as electrical conductivity and levels of dissolved organic C, basic cations, aluminum, Si, and sulfur in the soil solution were higher in the NT soil. Under both soil management systems, more than 90 % of the total soluble Al was complexed with organic compounds, with similar Al activity. No significant changes were detected by 2:1 clay mineral XRD analyses in terms of extension or intercalation of Al-hydroxy-polymers in the no-tilled in comparison to the conventionally tilled soil. In both soil management systems, Al and Si activities in the soil solution indicated thermodynamic stability of 2:1 clay minerals with partially occupied by hydroxy-Al, suggesting deceleration in the intercalation process and a tendency of transforming clay minerals from extensive into partial intercalation.

Chemical and structural characterization of soil humic substances under agroforestry and conventional systems

Studies have proven that the agroforestry systems in the semi-arid region of the State of Ceará, Brazil, induce an increase in soil organic C levels. Notwithstanding, there is no information if this increase also results in qualitative changes in different pools of soil organic matter. The objective of this study was to verify the possible chemical and structural alterations in fulvic and humic acids of a Luvisol in areas adopting agroforestry, traditional intensive cultivation and native forest in a long-term experiment conducted in the semi-arid region of Ceará State, Brazil. The study was conducted in an experimental area of the National Goat Research Center (Embrapa) in Sobral, CE. The following treatments were evaluated: agrosilvopasture (AGP), silvopasture (SILV), intensive cultivation under fallow (ICF), and areas with native forest (NF). Soil fulvic and humic acids fractions were extracted from the 0-6 and 6-12 cm layers and characterized by elemental composition, thermogravimetry and infrared spectroscopy analyses. The elemental composition analysis of humic acids confirmed the data found for fulvic acids, showing reduction in the C, H and N levels, followed by an increase in O contents in the AGP and ICF treatments over SILV and NF. In all treatments, except to SILV in the 0-6 cm layer, the percentage of mass loss was highest (300-600 °C) for humic acids in the thermally most stable region. Despite the similarity between infrared spectra, soil fulvic acids in the SILV treatment extracted from 6-12 cm depth decrease the absorption bands at 1708 and 1408 cm-1 followed by an increase in the absorption band at 1608 cm-1 attributed to aromatic C=C groups. This behavior suggests an increase in the aromatic character of the structure. The AGP and ICF treatments, which increase the soil tilling, favored the maintenance of humic substances with a more aromatic character in the soil than SILV and NF. The less aromatic humic substances in the SILV treatment resulted in an increase of exchange sites of soil organic matter, indicating improved nutrient cycling and maintenance of productivity in the system.

Virtual anthropology: A comparison between the performance of conventional X-ray and MDCT in investigating the trabecular structure of long bones.

Recently, modern cross-sectional imaging techniques such as multi-detector computed tomography (MDCT) have pioneered post mortem investigations, especially in forensic medicine. Such approaches can also be used to investigate bones non-invasively for anthropological purposes. Long bones are often examined in forensic cases because they are frequently discovered and transferred to medico-legal departments for investigation. To estimate their age, the trabecular structure must be examined. This study aimed to compare the performance of MDCT with conventional X-rays to investigate the trabecular structure of long bones. Fifty-two dry bones (24 humeri and 28 femora) from anthropological collections were first examined by conventional X-ray, and then by MDCT. Trabecular structure was evaluated by seven observers (two experienced and five inexperienced in anthropology) who analyzed images obtained by radiological methods. Analyses contained the measurement of one quantitative parameter (caput diameter of humerus and femur) and staging the trabecular structure of each bone. Preciseness of each technique was indicated by describing areas of trabecular destruction and particularities of the bones, such as pathological changes. Concerning quantitative parameters, the measurements demonstrate comparable results for the MDCT and conventional X-ray techniques. In contrast, the overall inter-observer reliability of the staging was low with MDCT and conventional X-ray. Reliability increased significantly when only the results of the staging performed by the two experienced observers were compared, particularly regarding the MDCT analysis. Our results also indicate that MDCT appears to be better suited to a detailed examination of the trabecular structure. In our opinion, MDCT is an adequate tool with which to examine the trabecular structure of long bones. However, adequate methods should be developed or existing methods should be adapted to MDCT.

Modeling a processive molecular motor: the conventional kinesin

We present a model that allows for the derivation of the experimentally accesible observables: spatial steps, mean velocity, stall force, useful power, efficiency and randomness, etc. as a function of the [adenosine triphosphate] concentration and an external load F. The model presents a minimum of adjustable parameters and the theoretical predictions compare well with the available experimental results.

Comparison between detailed digital and conventional soil maps of an area with complex geology

Since different pedologists will draw different soil maps of a same area, it is important to compare the differences between mapping by specialists and mapping techniques, as for example currently intensively discussed Digital Soil Mapping. Four detailed soil maps (scale 1:10.000) of a 182-ha sugarcane farm in the county of Rafard, São Paulo State, Brazil, were compared. The area has a large variation of soil formation factors. The maps were drawn independently by four soil scientists and compared with a fifth map obtained by a digital soil mapping technique. All pedologists were given the same set of information. As many field expeditions and soil pits as required by each surveyor were provided to define the mapping units (MUs). For the Digital Soil Map (DSM), spectral data were extracted from Landsat 5 Thematic Mapper (TM) imagery as well as six terrain attributes from the topographic map of the area. These data were summarized by principal component analysis to generate the map designs of groups through Fuzzy K-means clustering. Field observations were made to identify the soils in the MUs and classify them according to the Brazilian Soil Classification System (BSCS). To compare the conventional and digital (DSM) soil maps, they were crossed pairwise to generate confusion matrices that were mapped. The categorical analysis at each classification level of the BSCS showed that the agreement between the maps decreased towards the lower levels of classification and the great influence of the surveyor on both the mapping and definition of MUs in the soil map. The average correspondence between the conventional and DSM maps was similar. Therefore, the method used to obtain the DSM yielded similar results to those obtained by the conventional technique, while providing additional information about the landscape of each soil, useful for applications in future surveys of similar areas.

Ultrastructural changes of the internal limiting membrane removed during indocyanine green assisted peeling versus conventional surgery for idiopathic macular epiretinal membrane

Résumé : Introduction : L'objectif de cette étude était d'une part d'évaluer les caractéristiques histologiques des fragments cellulaires rétiniens attachés à la limitante interne après vitrectomie et pelage d'une membrane epirétinienne, et d'autre part de mettre en évidence des différences histologiques entre les cas opérés avec ou sans l'aide d'ICG dilué dans du glucose 5%. Méthodes Nous avons examiné rétrospectivement l'histologie de 88 spécimens de membranes épimaculaires contenant la limitante interne de la rétine, qui ont été enlevés chirurgicalement entre 1995 et 2003. L'analyse histologique a centré principalement l'attention sur la présence et les caractéristiques des fragments cellulaires rétiniens attachés à la limitante interne. L'analyse statistique a comparé les résultats entre le groupe I (chirurgie conventionnelle sans l'aide de l'ICG) et le groupe II (chirurgie à l'aide de l'ICG). Résultats Soixante et onze patients ont eu une vitrectomie sans l'aide de l'ICG (groupe I) et 17 avec l'aide de l'ICG (groupe II). Le nombre de débris de cellules de Müller à la surface rétinienne de la limitante interne était plus important dans le groupe I (sans ICG) que dans le groupe II (avec ICG) (40.8% versus 11.8% ; p = 0.024). Des larges fragments cellulaires rétiniens attachés à la limitante interne ont été plus fréquemment observés dans le groupe I (sans ICG) que dans le groupe II (avec ICG) (63.4% versus 23.5%; p= 0.003). Dans cinq (7%) cas du groupe I, de gros éléments cellulaires rétiniens ont été mis en évidence (des axones neuraux ou des vaisseaux sanguins). De tels éléments n'ont pas été retrouvés dans les spécimens du groupe II (avec ICG). Conclusions L'utilisation de l'ICG dilué dans du glucose 5% pour faciliter le pelage d'une membrane épimaculaire et notamment l'ablation de la limitante interne de la rétine semble diminuer de manière significative le nombre et la taille des débris des cellules de Muller adhérents à la face rétinienne de la membrane limitante interne de la rétine. Cette observation suggère que l'utilisation per-opératoire d'ICG dilué dans du glucose 5% facilite l'ablation de la limitante interne pendant la chirurgie de la membrane epirétinienne en diminuant l'adhérence de la limitante interne à la rétine.

The switch from conventional to atypical antipsychotic treatment should not be based exclusively on the presence of cognitive deficits. A pilot study in individuals with schizophrenia.

Background: Atypical antipsychotics provide better control of the negative and affective symptoms of schizophrenia when compared with conventional neuroleptics; nevertheless, their heightened ability to improve cognitive dysfunction remains a matter of debate. This study aimed to examine the changes in cognition associated with long-term antipsychotic treatment and to evaluate the effect of the type of antipsychotic (conventional versus novel antipsychotic drugs) on cognitive performance over time. Methods: In this naturalistic study, we used a comprehensive neuropsychological battery of tests to assess a sample of schizophrenia patients taking either conventional (n = 13) or novel antipsychotics (n = 26) at baseline and at two years after. Results: Continuous antipsychotic treatment regardless of class was associated with improvement on verbal fluency, executive functions, and visual and verbal memory. Patients taking atypical antipsychotics did not show greater cognitive enhancement over two years than patients taking conventional antipsychotics. Conclusions Although long-term antipsychotic treatment slightly improved cognitive function, the switch from conventional to atypical antipsychotic treatment should not be based exclusively on the presence of these cognitive deficits.

Comparison of the methodologies of paediatric peanut food challenges in England and Switzerland

Document Type: Meeting Abstract

Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

MHC class II expression is differentially regulated in plasmacytoid and conventional dendritic cells.

Major histocompatibility complex (MHC) class II-restricted antigen presentation is essential for the function of dendritic cells (DCs). We show here that plasmacytoid DCs (pDCs) differ from all other DC subsets with respect to expression of CIITA, the 'master regulator' of MHC class II genes. The gene encoding CIITA is controlled by three cell type-specific promoters: pI, pIII and pIV. With gene targeting in mice, we demonstrate that pDCs rely strictly on the B cell promoter pIII, whereas macrophages and all other DCs depend on pI. The molecular mechanisms driving MHC class II expression in pDCs are thus akin to those operating in lymphoid rather than myeloid cells.

Chiroptical measurement of chiral aggregates at liquid-liquid interface in centrifugal liquid membrane cell by Mueller matrix and conventional circular dichroism methods

The centrifugal liquid membrane (CLM) cell has been utilized for chiroptical studies of liquid-liquid interfaces with a conventional circular dichroism (CD) spectropolarimeter. These studies required the characterization of optical properties of the rotating cylindrical CLM glass cell, which was used under the high speed rotation. In the present study, we have measured the circular and linear dichroism (CD and LD) spectra and the circular and linear birefringence (CB and LB) spectra of the CLM cell itself as well as those of porphyrine aggregates formed at the liquid-liquid interface in the CLM cell, applying Mueller matrix measurement method. From the results, it was confirmed that the CLM-CD spectra of the interfacial porphyrin aggregates observed by a conventional CD spectropolarimeter should be correct irrespective of LD and LB signals in the CLM cell.

Ultrastructural changes of the internal limiting membrane removed during indocyanine green assisted peeling versus conventional surgery for idiopathic macular epiretinal membrane.

PURPOSE: To evaluate the histologic features of cellular retinal fragments on the internal limiting membrane (ILM) removed during idiopathic macular epiretinal membrane (MEM) peeling surgery with and without the aid of indocyanine green (ICG) diluted in 5% glucose. METHODS: ILM specimens removed from 88 eyes during idiopathic MEM surgery between 1995 and 2003 were reviewed retrospectively. Histologic analysis focused on the presence and characteristics of retinal fragments on the retinal surface of the ILM. Statistical analysis compared the results between group I (conventional surgery) and group II (ICG-assisted peeling). RESULTS: Seventy-one eyes underwent MEM surgery without the aid of ICG (group I) and seventeen underwent MEM ICG-assisted surgery (group II). The amount of Müller cell debris on the retinal surface of the ILM was more significant in the group I than in the group II (40.8 vs. 11.8; P = 0.024). Large fragments of Müller cells were more frequently observed in the group I (no ICG) than in the group II (ICG) (63.4 vs. 23.5%; P = 0.003). CONCLUSIONS: The use of ICG diluted with 5% glucose in ILM removal during MEM surgery was associated with less retinal debris attached to the retinal face of the ILM compared with surgery in which ICG was not used.