Comparaison de différents protocoles de spéciation séquentielle du phosphore dans des sédiments de rivière

Trois méthodes classiques de spéciation séquentielle du phosphore ont été appliquées aux sédiments de la rivière Sûre, à une sélection de ses affluents de taille variable, ainsi qu'aux sédiments du prébarrage Misère, un petit réservoir eutrophe situé sur la Sûre. Les protocoles comparés sont ceux de HIELTJES et LIJKLEMA (H et L), de PALUDAN et JENSEN (P et J) et de GOLTERMAN et BOOMAN (G et B).Le phosphore total des sédiments étudiés s'élève à 0,6 mg·P·g-1 séd. sec pour les petits sous-bassins expérimentaux (de l'ordre de 1 km2), à 0,8-1,0 mg·P·g-1 séd. sec pour les bassins de taille moyenne (20 à 320 km2) et à 1,8 mg·P·g-1 séd. sec pour le prébarrage Misère. Les schémas de (H et L) et de (P et J) reproduisent de façon similaire les différences qualitatives existant entre les sédiments. Toutefois les parts relatives des différentes fractions varient selon le protocole utilisé. Les rendements d'extraction obtenus avec le schéma de (G et B) sont sensiblement supérieurs aux deux autres méthodes et sont très liés aux teneurs en phosphore total des mêmes échantillons.Pour le P-labile, une bonne corrélation est obtenue entre les concentrations extraites selon les protocoles de (H et L) et (P et J) (R2 =0,84, P < 0,001) ; cependant les valeurs absolues sont 40 % supérieures pour le premier (H et L) qui utilise NH4Cl comme extractant au lieu de H2O. La fraction P- (Fe+Al) de (H et L) et la somme des fractions P-Fe et P-Al de (P et J) sont également bien corrélées (R2 =0,90, P < 0,001), mais avec des valeurs 30 % supérieures pour le second protocole (P et J) qui réalise l'extraction en deux étapes. La fraction P-Fe de (G et B) est moins bien corrélée à la fraction P-Fe de (P et J) (R2 =0,74, P < 0,01), et les résultats obtenus selon ces deux protocoles sont très éloignés en valeur absolue. Quant à la fraction P-Ca, les résultats du protocole de (G et B) ne sont ni corrélés ni similaires à ceux des deux autres schémas, en raison de la nature complètement différente des extractants appliqués.The Haute-Sûre river, with a rural watershed of 428 km2 is the principal entry of the Esch-sur-Sûre reservoir, which is mainly used for drinking-water supply. The role of particulate phosphorus (suspended matter and sediments) is important to maintain the trophic level of lakes, and in particular of reservoirs, often receiving higher external nutrient loads than natural lakes. Indeed, phosphorus flux in the Haute-Sûre basin occurs mainly in particulate form, closely linked to the hydrological and morphological conditions of its drainage basin. Several authors have shown that the fractionation of sedimentary phosphorus is strongly correlated with its bioavailability.This study was carried out in the framework of a larger project concerning the characterisation of the phosphorus from the sediments of the Sûre river watershed. The choice among the fractionation procedures described in literature and the comparison of the different results remains often difficult because of the different nature of the proposed extracting solutions, but also because of variable solid: liquid ratios, or the different exposure times proposed. Three traditional fractionation methods, HIELTJES and LIJKLEMA (H and L) (1980), PALUDAN and JENSEN (P and J) (1995) and GOLTERMAN and BOOMAN (G and B) (1988), were thus tested in the present study and applied to sediments from the Sûre river bed and a selection of its tributaries of variable size as well as to the Misère predam sediments, a small reservoir located upstream from the main reservoir.The first protocol (H and L) classes the sedimentary phosphorus in four fractions: labile-P obtained with a NO4C1 1M solution, (Fe+Al)-P with NaOH 0.1M as reagent, Ca-P with a HCl 0.5 M solution and residual-P obtained by difference of the three precedent fractions with total P. The second (P and J) separates sedimentary phosphorus in 6 fractions: labile-P extracted with H2O, Fe-P with a dithionite-bicarbonate solution (NaHCO3 0.11 M and Na2 S2 O4 0.11 M), Al-P with a NaOH 0.1 M solution after acidification of the supernatant to pH=1 and separation of the resultant precipitate, AH-P (humic acids - P) obtained after mineralisation (H2 SO4 /K2 SO4 sat. at 400°C) of the previous precipitate, Ca-P with a HCl 0.5 M solution, and finally residual-P after drying and mineralisation of the sediment having undergone all the previous steps (H2 SO4 /K2 SO4 sat. at 400°C). The third tested protocol (G and B) proposes chelates as extracting solutions: the fraction Fe-P with Ca-NTA/dithionite (CaCO3 0.04 M + NTA 0.02 M - Na2 S2 O4 0.045 M), and the Ca-P fraction with Na-EDTA 0.05 M at pH=8.The obtained results demonstrate a substantial difference between the sampled sediments. The total phosphorus content of the sampled sediments varied between 0.6 mg·P·g-1 dw for the small experimental basins (around 1 km2), 0.8 to 1.0 mg·P·g-1 dw for the medium-sized basins (20 to 320 km2) and 1.8 mg·P·g-1 dw for the Misère predam (lentic system). As regards the phosphorus fractionation, the (H and L) and the (P and J) procedures are concordant from the qualitative point of view, the relative importance of the different fractions varying nevertheless according to the used scheme. With the (G and B) method the extracted P fractions were highest. In relative terms (% P-fraction in relation to total-P), the sampled sediments have a very similar behaviour according to (G and B), the quantitative differences between samples being strongly correlated to their total phosphorus content.A good correlation was found between the labile-P fractions determined according to (H and L) and according to (P and J) (R2=0.84, P < 0.001) with however 40% higher values for (H and L). The P-(Fe+Al) fraction of (H and L) and the sum of the fractions P-Fe + P-Al of (P and J) are correlated as well (R2=0.90, P < 0.001) with 30% higher values for (P and J). Regarding the P-Fe fraction, the results obtained with the (G and B) and (P and J) protocols are correlated (R2=0.74, P < 0.01), but results are quantitatively quite different. The P-Ca fraction of the (G and B) protocol is badly correlated and very different from the two other procedures, because of the completely different nature of the extracting solutions

Nonmalignant Features Associated with Inherited Colorectal Cancer Syndromes-Clues for Diagnosis

Simple Summary: Familiarity with nonmalignant features and comorbidities of cancer predisposition syndromes may raise awareness and assist clinicians in the diagnosis and interpretation of molecular test results. Genetic predisposition to colorectal cancer (CRC) should be suspected mainly in young patients, in patients with significant family histories, multiple polyps, mismatch repair-deficient tumors, and in association with malignant or nonmalignant comorbidities. The aim of this review is to describe the main nonmalignant comorbidities associated with selected CRC predisposition syndromes that may serve as valuable diagnostic clues for clinicians and genetic professionals.& nbsp;Genetic diagnosis of affected individuals and predictive testing of their at-risk relatives, combined with intensive cancer surveillance, has an enormous cancer-preventive potential in these families. A lack of awareness may be part of the reason why the underlying germline cause remains unexplained in a large proportion of patients with CRC. Various extracolonic features, mainly dermatologic, ophthalmic, dental, endocrine, vascular, and reproductive manifestations occur in many of the cancer predisposition syndromes associated with CRC and polyposis. Some are mediated via the WNT, TGF-beta, or mTOR pathways. However the pathogenesis of most features is still obscure. Here we review the extracolonic features of the main syndromes, the existing information regarding their prevalence, and the pathways involved in their pathogenesis. This knowledge could be useful for care managers from different professional disciplines, and used to raise awareness, enable diagnosis, and assist in the process of genetic testing and interpretation

Rapid discrimination and classification of edible insect powders using ATR-FTIR spectroscopy combined with multivariate analysis

Insects are being proposed as an alternative way to ensure world''s food and feed security. Methods to determine edible insect powder''s origin and species will be needed for quality control purposes. Infrared spectroscopy has been extensively used in rapid chemical fingerprinting of food products. The present research explores a new approach to discriminate and classify commercial edible insect powders using attenuated total reflectance mid-infrared spectroscopy combined with multivariate analysis. Infrared spectra of seven commercial edible insect powders from different species (Tenebrio molitor, Alphitobius diaperinus, Gryllodes sigillatus, Acheta domesticus and Locusta migratoria) and origins (the Netherlands and New Zealand) were collected to build up soft independent modelling of class analogy (SIMCA) models. SIMCA models clearly discriminated insects by their species and origin linking their differences to lipids and chitin. SIMCA models performance was tested using five spectra of each class not used to build up the training set. 100% correct predictions were obtained for all the samples analysed with the exception of one sample of Alphitobius diaperinus. Infrared spectroscopy coupled to multivariate analysis provided a powerful method for the assurance of insect powder''s authenticity

MCM9 is associated with germline predisposition to early-onset cancer-clinical evidence

Mutated MCM9 has been associated with primary ovarian insufficiency. Although MCM9 plays a role in genome maintenance and has been reported as a candidate gene in a few patients with inherited colorectal cancer (CRC), it has not been clearly established as a cancer predisposition gene. We re-evaluated family members with MCM9-associated fertility problems. The heterozygote parents had a few colonic polys. Three siblings had early-onset cancer: one had metastatic cervical cancer and two had early-onset CRC. Moreover, a review of the literature on MCM9 carriers revealed that of nine bi-allelic carriers reported, eight had early-onset cancer. We provide clinical evidence for MCM9 as a cancer germline predisposition gene associated with early-onset cancer and polyposis, mainly in a recessive inheritance pattern. These observations, coupled with the phenotype in knockout mice, suggest that diagnostic testing for polyposis, CRC, and infertility should include MCM9 analysis. Early screening protocols may be beneficial for carriers.Hereditary cancer genetic

CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells

The persistence of HIV reservoirs, including latently infected, resting CD4+ T cells, is the major obstacle to cure HIV infection. CD32a expression was recently reported to mark CD4+ T cells harboring a replication-competent HIV reservoir during antiretroviral therapy (ART) suppression. We aimed to determine whether CD32 expression marks HIV latently or transcriptionally active infected CD4+ T cells. Using peripheral blood and lymphoid tissue of ART-treated HIV+ or SIV+ subjects, we found that most of the circulating memory CD32+ CD4+ T cells expressed markers of activation, including CD69, HLA-DR, CD25, CD38, and Ki67, and bore a TH2 phenotype as defined by CXCR3, CCR4, and CCR6. CD32 expression did not selectively enrich for HIV- or SIV-infected CD4+ T cells in peripheral blood or lymphoid tissue; isolated CD32+ resting CD4+ T cells accounted for less than 3% of the total HIV DNA in CD4+ T cells. Cell-associated HIV DNA and RNA loads in CD4+ T cells positively correlated with the frequency of CD32+ CD69+ CD4+ T cells but not with CD32 expression on resting CD4+ T cells. Using RNA fluorescence in situ hybridization, CD32 coexpression with HIV RNA or p24 was detected after in vitro HIV infection (peripheral blood mononuclear cell and tissue) and in vivo within lymph node tissue from HIV-infected individuals. Together, these results indicate that CD32 is not a marker of resting CD4+ T cells or of enriched HIV DNA–positive cells after ART; rather, CD32 is predominately expressed on a subset of activated CD4+ T cells enriched for transcriptionally active HIV after long-term ART

Integrating clinical, molecular, proteomic and histopathological data within the tissue context : tissunomics

Malignant tumours show a marked degree of morphological, molecular and proteomic heterogeneity. This variability is closely related to microenvironmental factors and the location of the tumour. The activation of genetic alterations is very tissue-dependent and only few tumours have distinct genetic alterations. Importantly, the activation state of proteins and signaling factors is heterogeneous in the primary tumour and in metastases and recurrences. The molecular diagnosis based only on genetic alterations can lead to treatments with unpredictable responses, depending on the tumour location, such as the tumour response in melanomas versus colon carcinomas with mutations. Therefore, we understand that the correct evaluation of tumours requires a system that integrates both morphological, molecular and protein information in a clinical and pathological context, where intratumoral heterogeneity can be assessed. Thus, we propose the term 'tissunomics', where the diagnosis will be contextualised in each tumour based on the complementation of the pathological, molecular, protein expression, environmental cells and clinical data

Five microRNAs in Serum Are Able to Differentiate Breast Cancer Patients From Healthy Individuals

Breast cancer is the cancer with the most incidence and mortality in women. microRNAs are emerging as novel prognosis/diagnostic tools. Our aim was to identify a serum microRNA signature useful to predict cancer development. We focused on studying the expression levels of 30 microRNAs in the serum of 96 breast cancer patients vs. 92 control individuals. Bioinformatic studies provide a microRNA signature, designated as a predictor, based on the expression levels of five microRNAs. Then, we tested the predictor in a group of 60 randomly chosen women. Lastly, a proteomic study unveiled the overexpression and downregulation of proteins differently expressed in the serum of breast cancer patients vs. that of control individuals. Twenty-six microRNAs differentiate cancer tissue from healthy tissue, and 16 microRNAs differentiate the serum of cancer patients from that of the control group. The tissue expression of miR-99a, miR-497, miR-362, and miR-1274, and the serum levels of miR-141 correlated with patient survival. Moreover, the predictor consisting of miR-125b, miR-29c, miR-16, miR-1260, and miR-451 was able to differentiate breast cancer patients from controls. The predictor was validated in 20 new cases of breast cancer patients and tested in 60 volunteer women, assigning 11 out of 60 women to the cancer group. An association of low levels of miR-16 with a high content of CD44 protein in serum was found. Circulating microRNAs in serum can represent biomarkers for cancer prediction. Their clinical relevance and the potential use of the predictor here described are discussed

BMP2/BMP4 colorectal cancer susceptibility loci in northern and southern european populations

Genome-wide association studies have successfully identified 20 colorectal cancer susceptibility loci. Amongst these, four of the signals are defined by tagging single nucleotide polymorphisms (SNPs) on regions 14q22.2 (rs4444235 and rs1957636) and 20p12.3 (rs961253 and rs4813802). These markers are located close to two of the genes involved in bone morphogenetic protein (BMP) signaling (BMP4 and BMP2, respectively). By investigating these four SNPs in an initial cohort of Spanish origin, we found substantial evidence that minor allele frequencies (MAFs) may be different in northern and southern European populations. Therefore, we genotyped three additional southern European cohorts comprising a total of 2028 cases and 4273 controls. The meta-analysis results show that only one of the association signals (rs961253) is effectively replicated in the southern European populations, despite adequate power to detect all four. The other three SNPs (rs4444235, rs1957636 and rs4813802) presented discordant results in MAFs and linkage disequilibrium patterns between northern and southern European cohorts. We hypothesize that this lack of replication could be the result of differential tagging of the functional variant in both sets of populations. Were this true, it would have complex consequences in both our ability to understand the nature of the real causative variants, as well as for further study designs

Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer

Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial CRC. An integrated analysis of germline and tumor whole-exome sequencing data was performed in 18 unrelated CRC families. Deleterious single nucleotide variants (SNV), short insertions and deletions (indels), copy number variants (CNVs) and loss of heterozygosity (LOH) were assessed as candidates for first germline or second somatic hits. Candidate tumor suppressor genes were selected when alterations were detected in both germline and somatic DNA, fulfilling Knudson's two-hit hypothesis. Somatic mutational profiling and signature analysis were also performed. A series of germline-somatic variant pairs were detected. In all cases, the first hit was presented as a rare SNV/indel, whereas the second hit was either a different SNV (3 genes) or LOH affecting the same gene (141 genes). BRCA2, BLM, ERCC2, RECQL, REV3L and RIF1 were among the most promising candidate genes for germline CRC predisposition. The identification of new candidate genes involved in familial CRC could be achieved by our integrated analysis. Further functional studies and replication in additional cohorts are required to confirm the selected candidates