Mechanics of loop formation in plain weft knitting machinery

2022 ◽  
pp. 67-93
Author(s):  
Subrata Ghosh ◽  
Roopam Chauhan ◽  
Sukumar Roy
Keyword(s):  
Loop Formation

Point Defect Absorption and Dislocation Loop Formation at Grain Boundaries in Hvem-Irradiated Zr and Its Alloys:1. Influence of Solute Addition

1985 ◽  
Vol 43 ◽  
pp. 350-351
Author(s):  
R.A. Herring ◽  
M. Griffiths ◽  
M.H Loretto ◽  
R.E. Smallman
Keyword(s):  
Grain Boundary ◽  
Grain Boundaries ◽  
Point Defect ◽  
Reactor Core ◽  
Solute Concentration ◽  
Nuclear Industry ◽  
Dislocation Loops ◽  
Loop Formation ◽  
Component Material ◽  
Impurity Interaction

Because Zr is used in the nuclear industry to sheath fuel and as structural component material within the reactor core, it is important to understand Zr's point defect properties. In the present work point defect-impurity interaction has been assessed by measuring the influence of grain boundaries on the width of the zone denuded of dislocation loops in a series of irradiated Zr alloys. Electropolished Zr and its alloys have been irradiated using an AEI EM7 HVEM at 1 MeV, ∼675 K and ∼10-6 torr vacuum pressure. During some HVEM irradiations it has been seen that there is a difference in the loop nucleation and growth behaviour adjacent to the grain boundary as compared with the mid-grain region. The width of the region influenced by the presence of the grain boundary should be a function of the irradiation temperature, dose rate, solute concentration and crystallographic orientation.

scholarly journals Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin

2021 ◽  
Vol 7 (11) ◽  
pp. eabd6030
Author(s):  
Isabel Strohkendl ◽  
Fatema A. Saifuddin ◽  
Bryan A. Gibson ◽  
Michael K. Rosen ◽  
Rick Russell ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Eukaryotic Cells ◽  
Loop Formation ◽  
Chromatin Compaction ◽  
Dna Targeting ◽  
Genomic Regions ◽  
Dna Bendability ◽  
Nucleosome Arrays

Genome engineering nucleases must access chromatinized DNA. Here, we investigate how AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates target accessibility to Cas12a and determines the extent to which both steps of binding—PAM recognition and R-loop formation—are inhibited by the nucleosome. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing target-proximal dCas9 enhances DNA cleavage rates over 10-fold. Unexpectedly, Cas12a readily cleaves internucleosomal linker DNA within chromatin-like, phase-separated nucleosome arrays. DNA targeting is reduced only ~5-fold due to neighboring nucleosomes and chromatin compaction. This work explains the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted genomic regions in cells. We conclude that nucleosome unwrapping regulates accessibility to CRISPR-Cas nucleases and propose that increasing nucleosome breathing dynamics will improve DNA targeting in eukaryotic cells.

scholarly journals Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bo Zhang ◽  
Diyin Luo ◽  
Yu Li ◽  
Vanja Perčulija ◽  
Jing Chen ◽  
...  
Keyword(s):  
Genome Editing ◽  
Dna Cleavage ◽  
Binary Complex ◽  
Loop Formation ◽  
Dna Duplex ◽  
Target Dna ◽  
Before And After ◽  
Dna Strand ◽  
Type V ◽  
Functionally Diverse

AbstractCas12i is a newly identified member of the functionally diverse type V CRISPR-Cas effectors. Although Cas12i has the potential to serve as genome-editing tool, its structural and functional characteristics need to be investigated in more detail before effective application. Here we report the crystal structures of the Cas12i1 R-loop complexes before and after target DNA cleavage to elucidate the mechanisms underlying target DNA duplex unwinding, R-loop formation and cis cleavage. The structure of the R-loop complex after target DNA cleavage also provides information regarding trans cleavage. Besides, we report a crystal structure of the Cas12i1 binary complex interacting with a pseudo target oligonucleotide, which mimics target interrogation. Upon target DNA duplex binding, the Cas12i1 PAM-interacting cleft undergoes a remarkable open-to-closed adjustment. Notably, a zipper motif in the Helical-I domain facilitates unzipping of the target DNA duplex. Formation of the 19-bp crRNA-target DNA strand heteroduplex in the R-loop complexes triggers a conformational rearrangement and unleashes the DNase activity. This study provides valuable insights for developing Cas12i1 into a reliable genome-editing tool.

Effect of Laser Thermal Processing on Defect Evolution in Silicon

2002 ◽  
Vol 717 ◽  
Author(s):  
Erik Kuryliw ◽  
Kevin S. Jones ◽  
David Sing ◽  
Michael J. Rendon ◽  
Somit Talwar
Keyword(s):  
Point Defects ◽  
Thermal Processing ◽  
Defect Formation ◽  
Secondary Ion Mass Spectrometry ◽  
Laser Energy ◽  
Process Window ◽  
Loop Formation ◽  
Transmission Electron ◽  
Ultra Shallow Junctions ◽  
Laser Thermal Processing

AbstractLaser Thermal Processing (LTP) involves laser melting of an implantation induced preamorphized layer to form highly doped ultra shallow junctions in silicon. In theory, a large number of interstitials remain in the end of range (EOR) just below the laser-formed junction. There is also the possibility of quenching in point defects during the liquid phase epitaxial regrowth of the melt region. Since post processing anneals are inevitable, it is necessary to understand both the behavior of these interstitials and the nature of point defects in the recrystallized-melt region since they can directly affect deactivation and enhanced diffusion. In this study, an amorphizing 15 keV 1 x 1015/cm2 Si+ implant was done followed by a 1 keV 1 x 1014/cm2 B+ implant. The surface was then laser melted at energy densities between 0.74 and 0.9 J/cm2 using a 308 nm excimer-laser. It was found that laser energy densities above 0.81 J/cm2 melted past the amorphous-crystalline interface. Post-LTP furnace anneals were performed at 750°C for 2 and 4 hours. Transmission electron microscopy was used to analyze the defect formation after LTP and following furnace anneals. Secondary ion mass spectrometry measured the initial and final boron profiles. It was observed that increasing the laser energy density led to increased dislocation loop formation and increased diffusion after the furnace anneal. A maximum loop density and diffusion was observed at the end of the process window, suggesting a correlation between the crystallization defects and the interstitial evolution.

scholarly journals Short antisense oligonucleotides alleviate the pleiotropic toxicity of RNA harboring expanded CGG repeats

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Magdalena Derbis ◽  
Emre Kul ◽  
Daria Niewiadomska ◽  
Michał Sekrecki ◽  
Agnieszka Piasecka ◽  
...  
Keyword(s):  
Motor Behavior ◽  
Neurodegenerative Disorder ◽  
Therapeutic Potential ◽  
Cell Damage ◽  
Fragile X ◽  
Nuclear Proteins ◽  
Mirna Biogenesis ◽  
Loop Formation ◽  
Cgg Repeats ◽  
Initiation Of Translation

AbstractFragile X-associated tremor/ataxia syndrome (FXTAS) is an incurable neurodegenerative disorder caused by expansion of CGG repeats in the FMR1 5’UTR. The RNA containing expanded CGG repeats (rCGGexp) causes cell damage by interaction with complementary DNA, forming R-loop structures, sequestration of nuclear proteins involved in RNA metabolism and initiation of translation of polyglycine-containing protein (FMRpolyG), which forms nuclear insoluble inclusions. Here we show the therapeutic potential of short antisense oligonucleotide steric blockers (ASOs) targeting directly the rCGGexp. In nuclei of FXTAS cells ASOs affect R-loop formation and correct miRNA biogenesis and alternative splicing, indicating that nuclear proteins are released from toxic sequestration. In cytoplasm, ASOs significantly decrease the biosynthesis and accumulation of FMRpolyG. Delivery of ASO into a brain of FXTAS mouse model reduces formation of inclusions, improves motor behavior and corrects gene expression profile with marginal signs of toxicity after a few weeks from a treatment.

scholarly journals The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Evi Goulielmaki ◽  
Maria Tsekrekou ◽  
Nikos Batsiotos ◽  
Mariana Ascensão-Ferreira ◽  
Eleftheria Ledaki ◽  
...  
Keyword(s):  
Dna Damage ◽  
Rna Splicing ◽  
Excision Repair ◽  
Intron Retention ◽  
Dna Lesions ◽  
Splicing Factor ◽  
Loop Formation ◽  
Rna Targets ◽  
Underlying Mechanisms

AbstractRNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csbm/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders.

Androgen receptor: acting in the three-dimensional chromatin landscape of prostate cancer cells

2011 ◽  
Vol 5 (1) ◽  
Author(s):  
Harri Makkonen ◽  
Jorma J. Palvimo
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Cancer Cells ◽  
Binding Sites ◽  
Target Genes ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Loop Formation ◽  
Prostate Cancer Cells

AbstractAndrogen receptor (AR) acts as a hormone-controlled transcription factor that conveys the messages of both natural and synthetic androgens to the level of genes and gene programs. Defective AR signaling leads to a wide array of androgen insensitivity disorders, and deregulated AR function, in particular overexpression of AR, is involved in the growth and progression of prostate cancer. Classic models of AR action view AR-binding sites as upstream regulatory elements in gene promoters or their proximity. However, recent wider genomic screens indicate that AR target genes are commonly activated through very distal chromatin-binding sites. This highlights the importance of long-range chromatin regulation of transcription by the AR, shifting the focus from the linear gene models to three-dimensional models of AR target genes and gene programs. The capability of AR to regulate promoters from long distances in the chromatin is particularly important when evaluating the role of AR in the regulation of genes in malignant prostate cells that frequently show striking genomic aberrations, especially gene fusions. Therefore, in addition to the mechanisms of DNA loop formation between the enhancer bound ARs and the transcription apparatus at the target core promoter, the mechanisms insulating distally bound ARs from promiscuously making contacts and activating other than their normal target gene promoters are critical for proper physiological regulation and thus currently under intense investigation. This review discusses the current knowledge about the AR action in the context of gene aberrations and the three-dimensional chromatin landscape of prostate cancer cells.

scholarly journals Protein binding to a single termination-associated sequence in the mitochondrial DNA D-loop region.

1993 ◽  
Vol 13 (4) ◽  
pp. 2162-2171 ◽  
Author(s):  
C S Madsen ◽  
S C Ghivizzani ◽  
W W Hauswirth
Keyword(s):  
Mitochondrial Dna ◽  
Protein Binding ◽  
Loop Formation ◽  
Sequence Element ◽  
Conserved Sequence ◽  
Loop Region ◽  
In Organello ◽  
Close Proximity ◽  
D Loop

A methylation protection assay was used in a novel manner to demonstrate a specific bovine protein-mitochondrial DNA (mtDNA) interaction within the organelle (in organello). The protected domain, located near the D-loop 3' end, encompasses a conserved termination-associated sequence (TAS) element which is thought to be involved in the regulation of mtDNA synthesis. In vitro footprinting studies using a bovine mitochondrial extract and a series of deleted mtDNA templates identified a approximately 48-kDa protein which binds specifically to a single TAS element also protected within the mitochondrion. Because other TAS-like elements located in close proximity to the protected region did not footprint, protein binding appears to be highly sequence specific. The in organello and in vitro data, together, provide evidence that D-loop formation is likely to be mediated, at least in part, through a trans-acting factor binding to a conserved sequence element located 58 bp upstream of the D-loop 3' end.

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