Female mice carrying a defective Alox15 gene are protected from experimental colitis via sustained maintenance of the intestinal epithelial barrier function

Lipoxygenases (ALOXs) are involved in the regulation of cellular redox homeostasis. They also have been implicated in the biosynthesis of pro- and anti-inflammatory lipid mediators and play a role in the pathogenesis of inflammatory diseases, which constitute a major health challenge owing to increasing incidence and prevalence in all industrialized countries around the world. To explore the pathophysiological role of Alox15 (leukocyte-type 12-LOX) in mouse experimental colitis we tested the impact of systemic inactivation of the Alox15 gene on the extent of dextrane sulfate sodium (DSS) colitis. We found that in wildtype mice expression of the Alox15 gene was augmented during DSS-colitis while expression of other Alox genes (Alox5, Alox15b) was hardly altered. Systemic Alox15 (leukocyte-type 12-LOX) deficiency induced less severe colitis symptoms and suppressed in vivo formation of 12-hydroxyeicosatetraenoic acid (12-HETE), the major Alox15 (leukocyte-type 12-LOX) product in mice. These alterations were paralleled by reduced expression of pro-inflammatory gene products, by sustained expression of the zonula occludens protein 1 (ZO-1) and by a less impaired intestinal epithelial barrier function. These results are consistent with in vitro incubations of colon epithelial cells, in which addition of 12S-HETE compromised enantioselectively transepithelial electric resistance. Consistent with these data transgenic overexpression of human ALOX15 intensified the inflammatory symptoms. In summary, our results indicate that systemic Alox15 (leukocyte-type 12-LOX) deficiency protects mice from DSS-colitis. Since exogenous 12-HETE compromises the expression of the tight junction protein ZO-1 the protective effect has been related to a less pronounced impairment of the intestinal epithelial barrier function.     

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids

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Quantifying effects of soil heterogeneity on groundwater pollution at four sites in USA

Four sites located in the north-eastern region of the United States of America have been chosen to investigate the impacts of soil heterogeneity in the transport of solutes (bromide and chloride) through the vadose zone (the zone in the soil that lies below the root zone and above the permanent saturated groundwater). A recently proposed mathematical model based on the cumulative beta distribution has been deployed to compare and contrast the regions' heterogeneity from multiple sample percolation experiments. Significant differences in patterns of solute leaching were observed even over a small spatial scale, indicating that traditional sampling methods for solute transport, for example the gravity pan or suction lysimeters, or more recent inventions such as the multiple sample percolation systems may not be effective in estimating solute fluxes in soils when a significant degree of soil heterogeneity is present. Consequently, ignoring soil heterogeneity in solute transport studies will likely result in under- or overprediction of leached fluxes and potentially lead to serious pollution of soils and/or groundwater.The cumulative beta distribution technique is found to be a versatile and simple technique of gaining valuable information regarding soil heterogeneity effects on solute transport. It is also an excellent tool for guiding future decisions of experimental designs particularly in regard to the number of samples within one site and the number of sampling locations between sites required to obtain a representative estimate of field solute or drainage flux.     

Type I and Type II error under random-effects misspecification in generalized linear mixed models

Generalized linear mixed models (GLMMs) have become a frequently used tool for the analysis of non-Gaussian longitudinal data. Estimation is based on maximum likelihood theory, which assumes that the underlying probability model is correctly specified. Recent research is showing that the results obtained from these models are not always robust against departures from the assumptions on which these models are based. In the present work we have used simulations with a logistic random-intercept model to study the impact of misspecifying the random-effects distribution on the type I and II errors of the tests for the mean structure in GLMMs. We found that the misspecification can either increase or decrease the power of the tests, depending on the shape of the underlying random-effects distribution, and it can considerably inflate the type I error rate. Additionally, we have found a theoretical result which states that whenever a subset of fixed-effects parameters, not included in the random-effects structure equals zero, the corresponding maximum likelihood estimator will consistently estimate zero. This implies that under certain conditions a significant effect could be considered as a reliable result, even if the random-effects distribution is misspecified.     

Frequent genes in rare diseases: panel‐based next generation sequencing to disclose causal mutations in hereditary neuropathies

Hereditary neuropathies comprise a wide variety of chronic diseases associated to more than 80 genes identified to date. We herein examined 612 index patients with either a Charcot‐Marie‐Tooth phenotype, hereditary sensory neuropathy, familial amyloid neuropathy, or small fiber neuropathy using a customized multigene panel based on the next generation sequencing technique. In 121 cases (19.8%), we identified at least one putative pathogenic mutation. Of these, 54.4% showed an autosomal dominant, 33.9% an autosomal recessive, and 11.6% an X‐linked inheritance. The most frequently affected genes were PMP22 (16.4%), GJB1 (10.7%), MPZ, and SH3TC2 (both 9.9%), and MFN2 (8.3%). We further detected likely or known pathogenic variants in HINT1, HSPB1, NEFL, PRX, IGHMBP2, NDRG1, TTR, EGR2, FIG4, GDAP1, LMNA, LRSAM1, POLG, TRPV4, AARS, BIC2, DHTKD1, FGD4, HK1, INF2, KIF5A, PDK3, REEP1, SBF1, SBF2, SCN9A, and SPTLC2 with a declining frequency. Thirty‐four novel variants were considered likely pathogenic not having previously been described in association with any disorder in the literature. In one patient, two homozygous mutations in HK1 were detected in the multigene panel, but not by whole exome sequencing. A novel missense mutation in KIF5A was considered pathogenic because of the highly compatible phenotype. In one patient, the plasma sphingolipid profile could functionally prove the pathogenicity of a mutation in SPTLC2. One pathogenic mutation in MPZ was identified after being previously missed by Sanger sequencing. We conclude that panel based next generation sequencing is a useful, time‐ and cost‐effective approach to assist clinicians in identifying the correct diagnosis and enable causative treatment considerations.

     

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations

Cancer drug screening in patient‐derived cells holds great promise for personalized oncology and drug discovery but lacks standardization. Whether cells are cultured as conventional monolayer or advanced, matrix‐dependent organoid cultures influences drug effects and thereby drug selection and clinical success. To precisely compare drug profiles in differently cultured primary cells, we developed DeathPro, an automated microscopy‐based assay to resolve drug‐induced cell death and proliferation inhibition. Using DeathPro, we screened cells from ovarian cancer patients in monolayer or organoid culture with clinically relevant drugs. Drug‐induced growth arrest and efficacy of cytostatic drugs differed between the two culture systems. Interestingly, drug effects in organoids were more diverse and had lower therapeutic potential. Genomic analysis revealed novel links between drug sensitivity and DNA repair deficiency in organoids that were undetectable in monolayers. Thus, our results highlight the dependency of cytostatic drugs and pharmacogenomic associations on culture systems, and guide culture selection for drug tests.     

Quantifying effects of soil heterogeneity on groundwater pollution at four sites in USA

Four sites located in the north-eastern region of the United States of America have been chosen to investigate the impacts of soil heterogeneity in the transport of solutes (bromide and chloride) through the vadose zone (the zone in the soil that lies below the root zone and above the permanent saturated groundwater). A recently proposed mathematical model based on the cumulative beta distribution has been deployed to compare and contrast the regions' heterogeneity from multiple sample percolation experiments. Significant differences in patterns of solute leaching were observed even over a small spatial scale, indicating that traditional sampling methods for solute transport, for example the gravity pan or suction lysimeters, or more recent inventions such as the multiple sample percolation systems may not be effective in estimating solute fluxes in soils when a significant degree of soil heterogeneity is present. Consequently, ignoring soil heterogeneity in solute transport studies will likely result in     

A genome-wide RNAi screen to dissect centriole duplication and centrosome maturation in Drosophila

Centrosomes comprise a pair of centrioles surrounded by an amorphous pericentriolar material (PCM). Here, we have performed a microscopy-based genome-wide RNA interference (RNAi) screen in Drosophila cells to identify proteins required for centriole duplication and mitotic PCM recruitment. We analysed 92% of the Drosophila genome (13,059 genes) and identified 32 genes involved in centrosome function. An extensive series of secondary screens classified these genes into four categories: (1) nine are required for centriole duplication, (2) 11 are required for centrosome maturation, (3) nine are required for both functions, and (4) three genes regulate centrosome separation. These 32 hits include several new centrosomal components, some of which have human homologs. In addition, we find that the individual depletion of only two proteins, Polo and Centrosomin (Cnn) can completely block centrosome maturation. Cnn is phosphorylated during mitosis in a Polo-dependent manner, suggesting that the Polo-dependent phosphorylation of Cnn initiates centrosome maturation in flies.     

From drought sensing to developmental control: evolution of cyclic AMP signaling in social amoebas

Amoebas and other protists commonly encyst when faced with environmental stress. Although little is known of the signaling pathways that mediate encystation, the analogous process of spore formation in dictyostelid social amoebas is better understood. In Dictyostelium discoideum, secreted cyclic AMP (cAMP) mediates the aggregation of starving amoebas and induces the differentiation of prespore cells. Intracellular cAMP acting on cAMP-dependent protein kinase (PKA) triggers the maturation of spores and prevents their germination under the prevalent conditions of high osmolality in the spore head. The osmolyte-activated adenylate cyclase, ACG, produces cAMP for prespore differentiation and inhibition of spore germination. To retrace the origin of ACG function, we investigated ACG gene conservation and function in species that span the dictyostelid phylogeny. ACG genes, osmolyte-activated ACG activity, and osmoregulation of spore germination were detected in species that represent the 4 major groups of Dictyostelia. Unlike the derived species D. discoideum, many basal Dictyostelia have retained the ancestral mechanism of encystation from solitary amoebas. In these species and in solitary amoebas, encystation is independently triggered by starvation or by high osmolality. Osmolyte-induced encystation was accompanied by an increase in cAMP and prevented by inhibition of PKA, indicating that ACG and PKA activation mediate this response. We propose that high osmolality signals drought in soil amoebas and that developmental cAMP signaling in the Dictyostelia has evolved from this stress response.