Metformin strongly affects transcriptome of peripheral blood cells in healthy individuals

Funding Information: The study was supported by the European Regional Development Fund under the project ?Investigation of interplay between multiple determinants influencing response to metformin: search for reliable predictors for efficacy of type 2 diabetes therapy? (Project No.: 1.1.1.1/16/A/091, https://ec.europa.eu/regional_policy/en/funding/ erdf/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors would like to thank all the volunteers for their participation and acknowledge the Genome Database of the Latvian Population for providing biological material and data. Publisher Copyright: © 2019 Ustinova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Metformin is a commonly used antihyperglycaemic agent for the treatment of type 2 diabetes mellitus. Nevertheless, the exact mechanisms of action, underlying the various therapeutic effects of metformin, remain elusive. The goal of this study was to evaluate the alterations in longitudinal whole-blood transcriptome profiles of healthy individuals after a one-week metformin intervention in order to identify the novel molecular targets and further prompt the discovery of predictive biomarkers of metformin response. Next generation sequencing-based transcriptome analysis revealed metformin-induced differential expression of genes involved in intestinal immune network for IgA production and cytokine-cytokine receptor interaction pathways. Significantly elevated faecal sIgA levels during administration of metformin, and its correlation with the expression of genes associated with immune response (CXCR4, HLA-DQA1, MAP3K14, TNFRSF21, CCL4, ACVR1B, PF4, EPOR, CXCL8) supports a novel hypothesis of strong association between metformin and intestinal immune system, and for the first time provide evidence for altered RNA expression as a contributing mechanism of metformin’s action. In addition to universal effects, 4 clusters of functionally related genes with a subject-specific differential expression were distinguished, including genes relevant to insulin production (HNF1B, HNF1A, HNF4A, GCK, INS, NEUROD1, PAX4, PDX1, ABCC8, KCNJ11) and cholesterol homeostasis (APOB, LDLR, PCSK9). This inter-individual variation of the metformin effect on the transcriptional regulation goes in line with well-known variability of the therapeutic response to the drug.publishersversionPeer reviewe

The role of rock joint frictional strength in the containment of fracture propagation

The fracturing phenomenon within the reservoir environment is a complex process that is controlled by several factors and may occur either naturally or by artificial drivers. Even when deliberately induced, the fracturing behaviour is greatly influenced by the subsurface architecture and existing features. The presence of discontinuities such as joints, artificial and naturally occurring faults and interfaces between rock layers and microfractures plays an important role in the fracturing process and has been known to significantly alter the course of fracture growth. In this paper, an important property (joint friction) that governs the shear behaviour of discontinuities is considered. The applied numerical procedure entails the implementation of the discrete element method to enable a more dynamic monitoring of the fracturing process, where the joint frictional property is considered in isolation. Whereas fracture propagation is constrained by joints of low frictional resistance, in non-frictional joints, the unrestricted sliding of the joint plane increases the tendency for reinitiation and proliferation of fractures at other locations. The ability of a frictional joint to suppress fracture growth decreases as the frictional resistance increases; however, this phenomenon exacerbates the influence of other factors including in situ stresses and overburden conditions. The effect of the joint frictional property is not limited to the strength of rock formations; it also impacts on fracturing processes, which could be particularly evident in jointed rock masses or formations with prominent faults and/or discontinuities

Going Deeper: Metagenome of a Hadopelagic Microbial Community

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre

Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which in part are supplied by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities

Fracture growth leading to mechanical spalling around deposition boreholes of an underground nuclear waste repository

This study presents a three-dimensional numerical analysis of multiple fracture growth leading to spalling around nuclear waste deposition boreholes. Mechanical spalling due to stress amplification after drilling is simulated using a finite element-based fracture growth simulator. Fractures initiate in tension based on a damage criterion and grow by evaluating stress intensity factors at each fracture tip. Tip propagation is multi-modal, resulting in final fracture patterns that are representative of both tensile and shear failure. Their geometries are represented by smooth parametric surfaces, which evolve during growth using lofting. The corresponding surface and volumetric meshes are updated at every growth step to accommodate the evolving fracture geometries. The numerical model is validated by comparing simulated fracture patterns against those observed in the AECL Underground Rock Laboratory Mine-By Experiment. It is subsequently calibrated to simulate fracture initiation and growth around boreholes drilled in the Forsmark granodiorite, subjected to a far-field anisotropic triaxial stress that corresponds to the in situ stress model from the Swedish Forsmark site. The deposition tunnel is implicitly simulated by attaching the deposition borehole to a free domain boundary. Several geomechanical cases are investigated, in which fracture growth is numerically evaluated as a function of in situ stress state, tunnel orientation, borehole geometry, total number of boreholes and borehole spacing. Numerical results show that spalling occurs in all cases, given the underground conditions at Forsmark, with borehole geometry, spacing and stresses affecting the extent of fracture nucleation and growth patterns. The uncertainty in underground stress conditions is evaluated through varying stress magnitudes and orientations relative to the tunnel floor. Whereas tunnel orientation influences the relative locations where fractures initiate with respect to the tunnel floor, fracture growth and its final extent is determined by the relative magnitudes of the in situ stresses. Higher stress differential causes higher spalling depths, but in all cases, failure extent is localised to the borehole vicinity, not exceeding one borehole radius. The cylindrical borehole is modified at the top to provide an access ramp for the spent fuel canisters and fracture growth around several deposition boreholes is simulated for borehole tops having cylindrical, conical, and wedge shapes. The enlargement of the borehole top induces higher stress concentrations at the borehole–tunnel junction, increasing the severity of spalling closer to the tunnel floor. Massive failure occurs when a multiple borehole model is considered and the inter-borehole distance is small enough that adjacent “spalled” areas interact. At Forsmark, through-going fractures are predicted to develop when the borehole spacing is less than 4 m. The effect of spalling on the structural integrity of the deposition boreholes is illustrated for each test case and quantified in terms of maximum spalling depth, spalling width and total fractured surface area

Investigating Effects of Fracture Aperture and Orientation on the Behaviour of Weak Rock Using Discrete Element Method

The effects of the fracture aperture and orientation on the behaviour of weak rock were numerically investigated using discrete element method (DEM). In this study, the mechanical behaviour of the intact and fractured rock specimens was simulated by adopting the discontinuum based software PFC3D. The rock specimens with various fracture apertures and orientations were replicated, and the effects of these two fracture characteristics were studied through triaxial tests. The flat-joint model was employed for simulating the stress-strain behaviour of intact rock and had the ability to reproduce the cementation effect. The smooth-joint contact model was utilised to simulate the sliding effect of the fractures. The effects of five different fracture orientations were investigated in the combination of three different fracture aperture categories, namely very tight, open, and moderately wide. It can be concluded that the strength of the fractured weak rock specimens reduces as the fracture aperture width increases. The amount of alternation in strength and deformability that were contributed by fracture apertures differed with the orientations of the fracture. With the fracture orientation that was parallel to the deviatoric loading, the effect of fracture aperture on the strength and deformability of the specimens was less evident