Humusica 1, article 2 : Essential bases-Functional considerations

Humusica 1 and 2 Applied Soil Ecology Special issues are field guides for humipedon classification. Contrary to other similar manuals dedicated to soil, the objects that one can describe with these guides are living, dynamic, functional, and relatively independent soil units. This is the reason to why the authors dedicated the whole article number 2 to functional considerations even before readers could go in the field and face the matter to be classified. Experienced lectors can overstep many of the sections reported in this article. If the titles of sections "1 A functional classification", "2 What is a humus system?" and "3 Energetic considerations in terrestrial systems" stimulate the reader's curiosity, then we suggest to pass through them. Otherwise, only section "4 Climatic, plant litter, or nutritional constraints?" is crucial. Readers will understand how the soil works in terms of litter and Carbon accumulation, which one(s) among climatic, vegetational, or geological factors that intervene and strongly affect the formation processes of terrestrial (oxygenated) soils. The article concludes with a debate about a tergiversated question: can temperature influence humus decomposition? Preceding statements were used for explaining how the biological soil net can store in the soil a maximum of energy in the form of SOM, by raising a plateau partially independent of climatic conditions.Peer reviewe

Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci

<p>Abstract</p> <p>Background</p> <p>Estimates suggest that up to 30% of colorectal cancers (CRC) may develop due to an increased genetic risk. The mean age at diagnosis for CRC is about 70 years. Time of disease onset 20 years younger than the mean age is assumed to be indicative of genetic susceptibility. We have compared high resolution tumor genome copy number variation (CNV) (Roche NimbleGen, 385 000 oligo CGH array) in microsatellite stable (MSS) tumors from two age groups, including 23 young at onset patients without known hereditary syndromes and with a median age of 44 years (range: 28-53) and 17 elderly patients with median age 79 years (range: 69-87). Our aim was to identify differences in the tumor genomes between these groups and pinpoint potential susceptibility loci. Integration analysis of CNV and genome wide mRNA expression data, available for the same tumors, was performed to identify a restricted candidate gene list.</p> <p>Results</p> <p>The total fraction of the genome with aberrant copy number, the overall genomic profile and the <it>TP53 </it>mutation spectrum were similar between the two age groups. However, both the number of chromosomal aberrations and the number of breakpoints differed significantly between the groups. Gains of 2q35, 10q21.3-22.1, 10q22.3 and 19q13.2-13.31 and losses from 1p31.3, 1q21.1, 2q21.2, 4p16.1-q28.3, 10p11.1 and 19p12, positions that in total contain more than 500 genes, were found significantly more often in the early onset group as compared to the late onset group. Integration analysis revealed a covariation of DNA copy number at these sites and mRNA expression for 107 of the genes. Seven of these genes, <it>CLC, EIF4E</it>, <it>LTBP4, PLA2G12A, PPAT</it>, <it>RG9MTD2</it>, and <it>ZNF574</it>, had significantly different mRNA expression comparing median expression levels across the transcriptome between the two groups.</p> <p>Conclusions</p> <p>Ten genomic loci, containing more than 500 protein coding genes, are identified as more often altered in tumors from early onset versus late onset CRC. Integration of genome and transcriptome data identifies seven novel candidate genes with the potential to identify an increased risk for CRC.</p

Computing the Fréchet Distance with a Retractable Leash

All known algorithms for the Fréchet distance between curves proceed in two steps: first, they construct an efficient oracle for the decision version; second, they use this oracle to find the optimum from a finite set of critical values. We present a novel approach that avoids the detour through the decision version. This gives the first quadratic time algorithm for the Fréchet distance between polygonal curves in (Formula presented.) under polyhedral distance functions (e.g., (Formula presented.) and (Formula presented.)). We also get a (Formula presented.)-approximation of the Fréchet distance under the Euclidean metric, in quadratic time for any fixed (Formula presented.). For the exact Euclidean case, our framework currently yields an algorithm with running time (Formula presented.). However, we conjecture that it may eventually lead to a faster exact algorithm

Carbon and methane cycling in arsenic-contaminated aquifers

Geogenic arsenic (As) contamination of groundwater is a health threat to millions of people worldwide, particularly in alluvial regions of South and Southeast Asia. Mitigation measures are often hindered by high heterogeneities in As concentrations, the cause(s) of which are elusive. Here we used a comprehensive suite of stable isotope analyses and hydrogeochemical parameters to shed light on the mechanisms in a typical high-As Holocene aquifer near Hanoi where groundwater is advected to a low-As Pleistocene aquifer. Carbon isotope signatures (δ$^{13}$C-CH$_{4}$, δ$^{13}$C-DOC, δ$^{13}$C-DIC) provided evidence that fermentation, methanogenesis and methanotrophy are actively contributing to the As heterogeneity. Methanogenesis occurred concurrently where As levels are high (>200 µg/L) and DOC-enriched aquitard pore water infiltrates into the aquifer. Along the flowpath to the Holocene/Pleistocene aquifer transition, methane oxidation causes a strong shift in δ$^{13}$C-CH$_{4}$ from -87‰ to +47‰, indicating high reactivity. These findings demonstrate a previously overlooked role of methane cycling and DOC infiltration in high-As aquifers

Functional Studies on Primary Tubular Epithelial Cells Indicate a Tumor Suppressor Role of SETD2 in Clear Cell Renal Cell Carcinoma

SET domain-containing 2 (SETD2) is responsible for the trimethylation of histone H3 lysine36 (H3K36me3) and is one of the genes most frequently mutated in clear cell renal cell carcinoma (ccRCC). It is located at 3p21, one copy of which is lost in the majority of ccRCC tumors, suggesting that SETD2 might function as a tumor suppressor gene. However, the manner in which loss of SETD2 contributes to ccRCC development has not been studied in renal primary tubular epithelial cells (PTECs). Therefore, we studied the consequences of SETD2 knockdown through lentiviral shRNA in human PTECs. Consistent with its known function, SETD2 knockdown (SETD-KD) led to loss of H3K36me3 in PTECs. In contrast to SETD2 wild-type PTECs, which have a limited proliferation capacity; the SETD2-KD PTECs continued to proliferate. The expression profiles of SETD2-KD PTECs showed a large overlap with the expression profile of early-passage, proliferating PTECs, whereas nonproliferating PTECs showed a significantly different expression profile. Gene set enrichment analysis revealed a significant enrichment of E2F targets in SETD2-KD and proliferating PTECs as compared with nonproliferating PTECs and in proliferating PTEC compared with SETD2-KD. The SETD2-KD PTECs maintained low expression of CDKN2A and high expression of E2F1, whereas their levels changed with continuing passages in untreated PTECs. In contrast to the nonproliferating PTECs, SETD2-KD PTECs showed no β-galactosidase staining, confirming the protection against senescence. Our results indicate that SETD2 inactivation enables PTECs to bypass the senescence barrier, facilitating a malignant transformation toward ccRCC