Testing for top‐down cascading effects in a biomass‐driven ecological network of soil invertebrates

1. To investigate the structural changes of a food‐web architecture, we considered real data coming from a soil food web in one abandoned pasture with former low‐pressure agriculture management and we reproduced the corresponding ecological network within a multi‐agent fully programmable modeling environment in order to simulate dynamically the cascading effects due to the removal of entire functional guilds.
2. We performed several simulations differing from each other for the functional implications. At the first trophic level, we simulated a removal of the prey, that is, herbivores and microbivores, while at the second trophic level, we simulated a removal of the predators, that is, omnivores and carnivores. The five main guilds were removed either separately or in combination.
3. The alteration in the food‐web architecture induced by the removal of entire functional guilds was the highest when the entire second trophic level was removed, while the removal of all microbivores caused an alteration in the food‐web structure of less than 5% of the total changes due to the removal of opportunistic and predatory species.
4. Omnivores alone account for the highest shifts in time of the numerical abundances of the remaining species, providing computational evidence of the importance of the degree of omnivory in the stabilization of soil biota.

     

Ensemble of Gene Signatures Identifies Novel Biomarkers in Colorectal Cancer Activated through PPARγ and TNFα Signaling

We describe a novel bioinformatic and translational pathology approach, gene Signature Finder Algorithm (gSFA) to identify biomarkers associated with Colorectal Cancer (CRC) survival. Here a robust set of CRC markers is selected by an ensemble method. By using a dataset of 232 gene expression profiles, gSFA discovers 16 highly significant small gene signatures. Analysis of dichotomies generated by the signatures results in a set of 133 samples stably classified in good prognosis group and 56 samples in poor prognosis group, whereas 43 remain unreliably classified. AKAP12, DCBLD2, NT5E and SPON1 are particularly represented in the signatures and selected for validation in vivo on two independent patients cohorts comprising 140 tumor tissues and 60 matched normal tissues. Their expression and regulatory programs are investigated in vitro. We show that the coupled expression of NT5E and DCBLD2 robustly stratifies our patients in two groups (one of which with 100% survival at five years). We show that NT5E is a target of the TNF-α signaling in vitro; the tumor suppressor PPARγ acts as a novel NT5E antagonist that positively and concomitantly regulates DCBLD2 in a cancer cell context-dependent manner.     

The effect of hydroxylated fatty acid-containing phospholipids in the remodeling of lipid membranes

The synthetic fatty acid 2-hydroxyoleic acid (2OHOA) is an antitumor drug that regulates membrane lipid composition and structure. An important effect of this drug is the restoration of sphingomyelin (SM) levels in cancer cell membranes, where the SM concentration is lower than in non-tumor cells. It is well known that free fatty acid concentration in cell membranes is lower than 5%, and that fatty acid excess is rapidly incorporated into phospholipids. In a recent work, we have considered the effect of free 2OHOA in model membranes in liquid ordered (Lo) and liquid disordered (Ld) phases, by using all-atom molecular dynamics. This study concerns membranes that are modified upon incorporation of 2OHOA into different phospholipids. 2OHOA-containing phospholipids have a permanent effect on lipid membranes, making a Ld membrane surface more compact and less hydrated, whereas the opposite effect is observed in Lo domains. Moreover, the hydroxyl group of fatty acid chains increases the propensity of Ld model membranes to form hexagonal or other non-lamellar structures. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.     

Distribution of organochlorine pesticides in crop growing in the province of Latina

Aim of this trial was to verify the occurrence and the distribution of organochlorine pesticides (OCPs) in soil, uptake and translocation by different crops growing in glasshouses with different level of pollutants. Residues of OCPs have been detected in soils and crops in the province of Latina, an intensively agricultural area of Lazio Region, in Italy. Dieldrin was quantified particularly in zucchini, cucumber, melon, tomato during a vegetation period. Sampling was carried out at three different times after transplanting. Roots, stem, Leaves and fruits were analysed separately. It would not be advisable to grow cucurbits in soil with OCPs residues > 0.100 mg/kg, to respect the RML admitted in UE in cucurbitaceous fruits.     

Induction of robust diabetes resistance and prevention of recurrent type 1 diabetes following islet transplantation by gene therapy

We have previously shown that the development of type 1 diabetes (T1D) can be prevented in nonobese diabetic (NOD) mice by reconstitution with autologous hemopoietic stem cells retrovirally transduced with viruses encoding MHC class II I-A beta-chain molecules associated with protection from the disease. In this study we examined whether a blockade of the programmed death-1 (PD-1)-programmed death ligand-1 (PD-L1) pathway, a major pathway known to control diabetes occurrence, could precipitate T1D in young NOD mice following reconstitution with autologous bone marrow retrovirally transduced with viruses encoding protective MHC class II I-A beta-chain molecules. In addition, we examined whether the expression of protective MHC class II alleles in hemopoietic cells could be used to prevent the recurrence of diabetes in mice with pre-existing disease following islet transplantation. Protection from the occurrence of T1D diabetes in young NOD mice by the expression of protective MHC class II I-A beta-chain molecules in bone marrow-derived hemopoietic cells was resistant to induction by PD-1-PD-L1 blockade. Moreover, reconstitution of NOD mice with pre-existing T1D autologous hemopoietic stem cells transduced with viruses encoding protective MHC class II I-A beta-chains allowed for the successful transplantation of syngeneic islets, resulting in the long-term reversal of T1D. Reversal of diabetes was resistant to induction by PD-1-PDL-1 blockade and depletion of CD25(+) T cells. These data suggest that expression of protective MHC class II alleles in bone marrow-derived cells establishes robust self-tolerance to islet autoantigens and is sufficient to prevent the recurrence of autoimmune diabetes following islet transplantation.     

Isolation and characterisation of bacterial colonies from seeds and in vitro cultures of Fraxinus spp. from Italian sites

Culturable bacteria were isolated from seeds, embryos and contaminated in vitro cultures of ash (Fraxinus excelsior L., F. ornus L. and F. angustifolia L.) and were identified using morphological and molecular analyses. Fourteen morphologically distinct isolates were recovered from seeds of Fraxinus spp. 16S rDNA sequencing categorised these isolates into ten separate genera. Three strains isolated from contaminated in vitro cultures, Pantoea agglomerans, Staphylococcus succinus and Aerococcus viridans, were used for comparative analysis with isolates from seeds. Antibiotic sensitivity testing of the isolated contaminants, including phytotoxicity of antibiotics on in vitro cultures of ash, was also investigated. Phytotoxic effects on explants immersed in ampicillin or cultured on medium containing ampicillin were negligible, however tetracycline, either alone or in combination with other antibiotics, had phytotoxic effects. We conclude that ampicillin is a suitable antibiotic to limit the growth of contaminating bacteria during the in vitro culture of ash.     

The expression of mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase supports a role in rapid cell growth

Deletion of the gene encoding NAD-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase (NMDMC) in mice was demonstrated previously to result in failure to establish definitive erythropoiesis in the developing liver. We examined the expression pattern of nmdmc to look for evidence that would support a tissue specific role for this activity. However, whole mount in situ hybridization revealed ubiquitous expression of nmdmc in the tissues of E9.5 and E10.5 embryos suggesting a broader role. Analysis of chimeras demonstrated that nmdmc-/- cells can survive in liver and other tissues of chimeras establishing that the null defect can be rescued by metabolites supplied by surrounding normal cells. Both the expression pattern and metabolite rescue support the proposal that mitochondrial NMDMC provides one-carbon units for purine synthesis during embryogenesis. The elevated expression of NMDMC in tumour cells, but not in surrounding normal cells, is predicted to result in significant differences in folate-mediated support for purine synthesis in the two cell types.