Experimental investigation and mechanism analysis on rock damage by high voltage spark discharge in water : effect of electrical conductivity

High voltage spark discharge (HVSD) could generate strong pressure waves that can be combined with a rotary drill bit to improve the penetration rate in unconventional oil and gas drilling. However, there has been little investigation of the effect of electrical conductivity on rock damage and the fragmentation mechanism caused by HVSD. Therefore, we conducted experiments to destroy cement mortar, a rock-like material, in water with five conductivity levels, from 0.5 mS/cm to 20 mS/cm. We measured the discharge parameters, such as breakdown voltage, breakdown delay time, and electrical energy loss, and investigated the damage mechanism from stress waves propagation using X-ray computed tomography. Our study then analyzed the influence of conductivity on the surface damage of the sample by the pore size distribution and the cumulative pore area, as well as studied the dependence of internal damage on conductivity by through-transmission ultrasonic inspection technique. The results indicated that the increase in electrical conductivity decreased the breakdown voltage and breakdown delay time and increased the energy loss, which led to a reduction in the magnitude of the pressure wave and, ultimately, reduced the sample damage. It is worth mentioning that the relationship between the sample damage and electrical conductivity is non-linear, showing a two-stage pattern. The findings suggest that stress waves induced by the pressure waves play a significant role in sample damage where pores and two types of tensile cracks are the main failure features. Compressive stresses close horizontal cracks inside the sample and propagate vertical cracks, forming the tensile cracks-I. Tensile stresses generated at the sample-water interface due to the reflection of stress waves produce the tensile cracks-II. Our study is the first to investigate the relationship between rock damage and electrical conductivity, providing insights to guide the design of drilling tools based on HVSD

Structure and mechanism of the CMR complex for CRISPR-Mediated antiviral immunity

The prokaryotic clusters of regularly interspaced palindromic repeats (CRISPR) system utilizes genomically encoded CRISPR RNA (crRNA), derived from invading viruses and incorporated into ribonucleoprotein complexes with CRISPR-associated (CAS) proteins, to target and degrade viral DNA or RNA on subsequent infection. RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse "payload" of targeting crRNA. The crystal structure of Cmr7 and low-resolution structure of the complex are presented. S. solfataricus CMR cleaves RNA targets in an endo-nucleolytic reaction at UA dinucleotides. This activity is dependent on the 8 nt repeat-derived 5' sequence in the crRNA, but not on the presence of a proto-spacer-associated motif (PAM) in the target. Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets.Publisher PDFPeer reviewe

Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes

The perivascular niche (PVN) plays an essential role in brain tumor stem-like cell (BTSC) fate control, tumor invasion, and therapeutic resistance. Here, a microvasculature-on-a-chip system as a PVN model is used to evaluate the ex vivo dynamics of BTSCs from ten glioblastoma patients. BTSCs are found to preferentially localize in the perivascular zone, where they exhibit either the lowest motility, as in quiescent cells, or the highest motility, as in the invasive phenotype, with migration over long distance. These results indicate that PVN is a niche for BTSCs, while the microvascular tracks may serve as a path for tumor cell migration. The degree of colocalization between tumor cells and microvessels varies significantly across patients. To validate these results, single-cell transcriptome sequencing (10 patients and 21 750 single cells in total) is performed to identify tumor cell subtypes. The colocalization coefficient is found to positively correlate with proneural (stem-like) or mesenchymal (invasive) but not classical (proliferative) tumor cells. Furthermore, a gene signature profile including PDGFRA correlates strongly with the “homing” of tumor cells to the PVN. These findings demonstrate that the model can recapitulate in vivo tumor cell dynamics and heterogeneity, representing a new route to study patient-specific tumor cell functions

Effects of Confining Pressure and Hydrostatic Pressure on the Fracturing of Rock under Cyclic Electrohydraulic Shock Waves

For an array of applications of the high voltage pulse discharge technology in reservoir stimulations and to gain a deeper understanding of the fractures mechanism of deep well rock under cyclic electrohydraulic shock waves (EHSWs), the effect of confining pressure and hydrostatic pressure on the fracturing of rock under EHSWs are investigated in this paper. Firstly, a two-dimensional (2D) water-explosive numerical model is built to match the computed peak pressure of the EHSW with that obtained by the empirical formula by tuning the relevant parameters, based on the equivalent method of EHSWs. Then, a rock model is established to obtain the stress distribution under static loads. Subsequently, the water-explosive model is coupled with the rock model to obtain the stress distribution under static and dynamic loads. In addition, based on this coupling model, the influences of confining pressure and hydrostatic pressure on circumferential stress, radial stress in the rock and the fracturing of rock around the wellbore are discussed. Finally, two improvement measures (increasing discharge energy and changing loading mode) are proposed to acquire greater fracture density based on intensive numerical simulations. The results show that the increase in hydrostatic pressure is beneficial to the crack formation and development, whereas confining pressure is harmful. Moreover, the inhibitory effect of confining pressure on crack formation is greater than the promotion effect of hydrostatic pressure on crack formation. Increasing the discharge energy can effectively promote the development of the number and length of main cracks. Under four repetitive loading modes with the same total discharge energy (1.36 × 15 kJ), the greatest fracture density can be obtained by using repetitive loading mode with a gradually decreasing mode of discharge energy (first level: 2 times (1.36 × 5 kJ); second level: 5 times (1.36 × 1 kJ))

A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication ▿ †

The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the Poxviridae and other large cytoplasmic eukaryotic viruses. Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between an active-site tyrosine and the 5′ end of the DNA, releasing a 3′ DNA end as a primer for DNA synthesis. The enzyme can also catalyze the joining reaction that is necessary to reseal the DNA hairpin and terminate replication. The dimeric structure points to a simple mechanism through which two closely positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral replication are discussed

Structural and Functional Characterisation of a Conserved Archaeal RadA Paralog with Antirecombinase Activity

DNA recombinases (RecA in bacteria, Rad51 in eukarya and RadA in archaea) catalyse strand-exchange between homologous DNA molecules, the central reaction of homologous recombination, and are among the most conserved DNA repair proteins known. In bacteria, RecA is the sole protein responsible for this reaction, whereas, in eukaryotes, there are several RAD51 paralogs that cooperate to catalyse strand exchange. All archaea have at least one (and as many as four) RadA paralogs, but their function remains unclear. Here we show the three RadA paralogs encoded by the Sulfolobus solfataricus genome are expressed under normal growth conditions, and are not UV-inducible. We demonstrate that one of these proteins, Sso2452, which is representative of the large aRadC sub-family of archaeal RadA paralogs, functions as an ATPase that binds tightly to ssDNA. However, Sso2452 is not an active recombinase in vitro, and inhibits D-loop formation by RadA. We present the high-resolution crystal structure of Sso2452, which reveals key structural differences from the canonical RecA family recombinases that may explain its functional properties. The possible roles of the archaeal RadA paralogs in vivo are discussed

Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity

The prokaryotic clusters of regularly interspaced palindromic repeats (CRISPR) system utilizes genomically encoded CRISPR RNA (crRNA), derived from invading viruses and incorporated into ribonucleoprotein complexes with CRISPR-associated (CAS) proteins, to target and degrade viral DNA or RNA on subsequent infection. RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse “payload” of targeting crRNA. The crystal structure of Cmr7 and low-resolution structure of the complex are presented. S. solfataricus CMR cleaves RNA targets in an endonucleolytic reaction at UA dinucleotides. This activity is dependent on the 8 nt repeat-derived 5′ sequence in the crRNA, but not on the presence of a protospacer-associated motif (PAM) in the target. Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets

Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE)

In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli “CRISPR-associated complex for antiviral defense” (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea