Chromosome Compaction by Active Loop Extrusion

During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they p rogressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process.National Institutes of Health (U.S.) (Grant GM114190)National Institutes of Health (U.S.) (Grant R01HG003143

DNA damage induced during mitosis undergoes DNA repair synthesis.

Understanding the mitotic DNA damage response (DDR) is critical to our comprehension of cancer, premature aging and developmental disorders which are marked by DNA repair deficiencies. In this study we use a micro-focused laser to induce DNA damage in selected mitotic chromosomes to study the subsequent repair response. Our findings demonstrate that (1) mitotic cells are capable of DNA repair as evidenced by DNA synthesis at damage sites, (2) Repair is attenuated when DNA-PKcs and ATM are simultaneously compromised, (3) Laser damage may permit the observation of previously undetected DDR proteins when damage is elicited by other methods in mitosis, and (4) Twenty five percent of mitotic DNA-damaged cells undergo a subsequent mitosis. Together these findings suggest that mitotic DDR is more complex than previously thought and may involve factors from multiple repair pathways that are better understood in interphase

Microbial induced corrosion by ferric–reducing bacteria isolated from an oil separation tank

Se requiere identificar a las poblaciones microbianas que participan en la Corrosión Inducida por Microorganismos, con la finalidad de implementar estrategias de monitoreo eficiente y de control. Las poblaciones de microorganismos anaerobios presentes en la industria petrolera, particularmente en la producción de gas y petróleo, así como en las líneas de transporte y en los tanques de almacenamiento, han sido estudiadas muy pobremente y los estudios presentes se han enfocado principalmente en bacterias sulfatorreductoras de los géneros Desulfovibrio y Desulfobacter. Sin embargo, las bacterias fermentativas también tienen gran relevancia en la corrosión de metales, como se describió en 1997, por el grupo de Magot y colaboradores, quienes caracterizaron una bacteria no sulfidogénica pero con capacidad de producir corrosión. En este estudio se aisló de un tanque de separación, una bacteria anaerobia, fermentativa y reductora de fierro, perteneciente al género Sedimentibacter, con capacidad de producir corrosión en el acero al carbón SAE1018.It has required the characterization and identification of the microbial populations responsible for Microbial Induced Corrosion (MIC), and their interactions with distinctive microorganisms allocated on metallic surfaces, in order to implement efficient monitoring and control strategies. Microbial anaerobic communities present at oil and gas producing, transporting and storage facilities have been poorly characterized and studies had mainly focused on Desulfovibrio and Desulfobacter genus. However, fermentative bacteria have important participation on corrosion metals as described by Magot et al. (1997), which characterization of non-SRB sulfidogenic bacteria was able to produce corrosion. In this study, it was isolated of an oil-water tank separation, an anaerobic bacterium, fermentative and ferric-reducing, belong to Sedimentibacter genus with corrosion capability on Carbon Steel SAE1018

MICROBIAL ABUNDANCE, DIVERSITY, AND POTENTIAL ACTIVITY IN BENTONITE CLAY

The Canadian deep geologic repository (DGR) concept for long-term safe storage and isolation of used nuclear fuel incorporates a multi-protective engineered barrier system. However, due to the inevitable presence of microorganisms and their metabolic products in a DGR, the integrity of the containers, and hence the repository, might be compromised. Therefore, the emphases of this thesis are to characterize and identify the microbial populations present in bulk and highly-compacted Wyoming MX-80 bentonite, to determine the conditions under which the survival and activity of microorganisms in highly-compacted bentonite clay (one of the engineered barriers) will be minimized or regulated, and to observe the microbial capacity to interact with bentonite particle under nutrient regime (clay-microbe aggregation study). To achieve these, culture-dependent and molecular biology methods (e.g., 16S rRNA sequencing), a range of analytical chemistry assays (e.g., sulfate turbidimetric method), pressure cell studies, microscopic technique (e.g., confocal laser microscopy (CLSM)), particle size analyses and laboratory-scale enrichment (or microcosm) assays were carried out. Culture-dependent techniques revealed the presence of spore-forming bacterial isolates belonging to phyla Actinobacteria and Firmicutes in bulk MX-80. Interestingly, when MX-80 bentonite was highly compacted, Gram-positive spore-formers were also identified after being exposed to the collective effect of > 2,000 kPa swelling pressure, 0.96 water activity, oxygen-free environment, and ≥ 1.6 g/cm3 dry density conditions for ~ 145 days and ~ 8 years. It was determined that microbial culturability was suppressed at or below background level (i.e., ≤ 2 x 102 Colony Forming Units per g) when the aforementioned parameters were applied and when 50 g/L NaCl solution infiltrated the highly-compacted bentonite (HCB). Sulfate reducing bacteria (SRB) in the HCB, however, were speculated to remain as spores during the incubation period since their microbial counts were similar at different dry densities. The enrichment assays for SRB containing bentonite clay slurry amended with carbon, electron donors and acceptors revealed that lactate was the preferred substrate for sulfidogenesis and that high salinity could impede the same process. Finally, the clay-microbe aggregation study showed that extracellular polymeric substance (EPS) contribute to the clay-microbe aggregation and that nutrient concentration, carbon substrate type and bentonite concentration affect EPS production. Overall, these studies are relevant to DGR operations because the results obtained will assist in understanding the potential consequences of microbial interactions with clay minerals

Drone-Based Identification of Erosive Processes in Open-Pit Mining Restored Areas

Altres ajuts: European Union LIFE20 PRE/IT/000007Unmanned Aerial Systems, or drones, are very helpful tools for managing open-pit mining operations and developing ecological restoration activities. This article presents a method for identifying water erosion processes in active quarries by means of drone imagery remote sensing, in the absence of pre-existing imagery or mapping for comparison. A Digital Elevation Model (DEM) with a spatial resolution (SR) >10 cm and an orthophoto with an SR >2.5 cm were generated from images captured with a drone and their subsequent photogrammetric processing. By using Geographical Information Systems tools to process the DEM, a detailed drainage network was obtained, the areas of detected water erosion were separated, and the watersheds in the gullies identified. Subsequently, an estimated DEM before the erosive processes was reconstructed by interpolating the gully ridges; this DEM serves as a reference for the relief before the erosion. To calculate the volume of eroded material, the DEM of Differences was calculated, which estimates the volume difference between the previously estimated DEM and the current DEM. Additionally, we calculated the material necessary for the geomorphological adaptation of the quarry and the slope map, which are two valuable factors closely related to the monitoring of erosive processes. The results obtained allowed us to identify the erosion factors quickly and accurately in this type of mining. In the case of water-filled quarries, it would be important to characterize the subsurface relief. Essentially, the presented method can be applied with affordable and non-invasive materials to create digital grid maps at 10 cm resolution, obtaining data ready for 3D metrics, being a very practical landscape modelling tool for characterizing the restoration evolution of open-pit mining spaces

Toward precision medicine with nanopore technology

Currently, when patients are diagnosed with cancer, they often receive a treatment based on the type and stage of the tumor. However, different patients may respond to the same treatment differently, due to the variation in their genomic alteration profile. Thus, it is essential to understand the effect of genomic alterations on cancer drug efficiency and engineer devices to monitor these changes for therapeutic response prediction. Nanopore-based detection technology features devices containing a nanometer-scale pore embedded in a thin membrane that can be utilized for DNA sequencing, biosensing, and detection of biological or chemical modifications on single molecules. Overall, this project aims to evaluate the capability of the biological nanopore, alpha-hemolysin, as a biosensor for genetic and epigenetic biomarkers of cancer. Specifically, we utilized the nanopore to (1) study the effect of point mutations on C-kit1 G-quadruplex formation and its response to CX-5461 cancer drug; (2) evaluate the nanopore\u27s ability to detect cytosine methylation in label-dependent and label-independent manners; and (3) detect circulating-tumor DNA collected from lung cancer patients\u27 plasma for disease detection and treatment response monitoring. Compared to conventional techniques, nanopore assays offer increased flexibility and much shorter processing time