Athma

BACKGROUND: To replace missing periodontal tissues in vertical defects during periodontal surgery, bone graft materials are frequently used. A frequent occurrence that can affect healing outcomes is postoperative edema. The purpose of this study was to evaluate postoperative edema in various vertical bone graft defects following periodontal surgery. MATERIALS AND METHODS: 50 participants were split into two groups for a prospective study: Group A received xenografts, whereas Group B received synthetic grafts...

The expression of a precise mRNA transcriptome is crucial for establishing cell identity and function, with dozens of alternative isoforms produced for a single gene sequence. The regulation of mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processing mechanisms across a gene. Decisions involved in mRNA initiation and termination underlie the largest extent of mRNA isoform diversity, but little is known about any relationships between decisions at both ends of mRNA molecules. Here, we systematically profile the joint usage of mRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues and species...

Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3' end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling...

Rational control of the reaction parameters is highly important for synthesizing active electrocatalysts. NiCo2 S4 is an excellent spinel-based electrocatalyst that is usually prepared through a two-step synthesis. Herein, a one-step hydrothermal route is reported to synthesize P-incorporated NiCo2 S4 . We discovered that the inclusion of P caused formation of the NiCo2 S4 phase in a single step. Computational studies were performed to comprehend the mechanism of phase formation and to examine the energetics of lattice formation...

No abstract text is available yet for this article.

Long-read sequencing (LRS) technologies have the potential to revolutionize scientific discoveries in RNA biology, especially by enabling the comprehensive identification and quantification of full length mRNA isoforms. However, inherently high error rates make the analysis of long-read sequencing data challenging. While these error rates have been characterized for sequence and splice site identification, it is still unclear how accurately LRS reads represent transcript start and end sites. Here, we systematically assess the variability and accuracy of mRNA terminal ends identified by LRS reads across multiple sequencing platforms...

The nuclear long non-coding RNA LUCAT1 has previously been identified as a negative feedback regulator of type I interferon and inflammatory cytokine expression in human myeloid cells. Here, we define the mechanistic basis for the suppression of inflammatory gene expression by LUCAT1. Using comprehensive identification of RNA-binding proteins by mass spectrometry as well as RNA immunoprecipitation, we identified proteins important in processing and alternative splicing of mRNAs as LUCAT1-binding proteins. These included heterogeneous nuclear ribonucleoprotein C, M, and A2B1...

Friedreich's ataxia is an incurable disease caused by frataxin (FXN) protein deficiency, which is mostly induced by GAA repeat expansion in intron 1 of the FXN gene. Here, we identified antisense oligonucleotides (ASOs), complementary to two regions within the first intron of FXN pre-mRNA, which could increase FXN mRNA by ∼2-fold in patient fibroblasts. The increase in FXN mRNA was confirmed by the identification of multiple overlapping FXN-activating ASOs at each region, two independent RNA quantification assays, and normalization by multiple housekeeping genes...

Cohesin-mediated loop extrusion has been shown to be blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent...

No abstract text is available yet for this article.

The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with beta cell proliferation. Recent studies have found that expression of circular species of ANRIL is linked to the regulation of cardiovascular phenotypes. Less is known about how the abundance of circular ANRIL may influence T2D phenotypes...

AIM: Anatomical landmarks that remain fairly constant throughout an individual's life help determine the position of the artificial teeth closer to that of their predecessors. The aim of the present study was to evaluate whether there is a relationship between the intercondylar widths (ICWs) and the interdental widths (IDWs) in the maxillary and mandibular arches in dentate subjects. MATERIALS AND METHODS: The study was conducted in two parts, with 80 dentate subjects in total...

Messenger RNA isoform differences are predominantly driven by alternative first, internal, and last exons. Despite the importance of classifying exons to understand isoform structure, few tools examine isoform-specific exon usage. We recently observed that alternative transcription start sites often arise near internal exons, often creating "hybrid" first/internal exons. To systematically detect hybrid exons, we built the hybrid-internal-terminal (HIT) pipeline to classify exons depending on their isoform-specific usage...

AIMS: To assess the effect of titanium dioxide nanoparticles (NPs) on flexural strength and cytotoxicity of heat-cured polymethyl methacrylate (PMMA) resins. METHODOLOGY: Sixty-four rectangular and 12 circular specimens were fabricated from metal dies to test flexural strength and cytotoxicity, respectively. The rectangular specimens were grouped into four (16 specimens each)-control group (Group 1), Group 2 with 3% TiO2 , Group 3 with 5% TiO2 , and Group 4 with 7% TiO2 ...

Adeno-associated virus (AAV) vectors are important delivery platforms for therapeutic genome editing but are severely constrained by cargo limits. Simultaneous delivery of multiple vectors can limit dose and efficacy and increase safety risks. Here, we describe single-vector, ~4.8-kb AAV platforms that express Nme2Cas9 and either two sgRNAs for segmental deletions, or a single sgRNA with a homology-directed repair (HDR) template. We also use anti-CRISPR proteins to enable production of vectors that self-inactivate via Nme2Cas9 cleavage...

Studies evaluating the association of IL-10 polymorphisms with risk of pediatric asthma found inconsistent data. Here, we performed a meta-analysis to get a precise estimation of the associations. Relevant studies identified in the PubMed, Scopus, CNKI databases were used to perform a meta-analysis. A total of 23 case-control studies including nine studies with 1298 cases and 1079 controls on -1082G > A, four studies with 622 cases and 603 controls on -819C > T and ten studies with 1480 case and 1462 controls on -592C > A were selected...

Sustained silencing of gene expression throughout the brain using small interfering RNAs (siRNAs) has not been achieved. Here we describe an siRNA architecture, divalent siRNA (di-siRNA), that supports potent, sustained gene silencing in the central nervous system (CNS) of mice and nonhuman primates following a single injection into the cerebrospinal fluid. Di-siRNAs are composed of two fully chemically modified, phosphorothioate-containing siRNAs connected by a linker. In mice, di-siRNAs induced the potent silencing of huntingtin, the causative gene in Huntington's disease, reducing messenger RNA and protein throughout the brain...

RNA processing has emerged as a key mechanistic step in the regulation of the cellular response to environmental perturbation. Recent work has uncovered extensive remodeling of transcriptome composition upon environmental perturbation and linked the impacts of this molecular plasticity to health and disease outcomes. These isoform changes and their underlying mechanisms are varied-involving alternative sites of transcription initiation, alternative splicing, and alternative cleavage at the 3' end of the mRNA...

Huntington's disease (HD) is a monogenic neurodegenerative disorder representing an ideal candidate for gene silencing with oligonucleotide therapeutics (i.e., antisense oligonucleotides [ASOs] and small interfering RNAs [siRNAs]). Using an ultra-sensitive branched fluorescence in situ hybridization (FISH) method, we show that ∼50% of wild-type HTT mRNA localizes to the nucleus and that its nuclear localization is observed only in neuronal cells. In mouse brain sections, we detect Htt mRNA predominantly in neurons, with a wide range of Htt foci observed per cell...

Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. However, detection of recursive splicing requires observation of splicing intermediates that are inherently unstable, making it difficult to study. Here we developed new computational approaches to identify recursively spliced introns and applied them, in combination with existing methods, to nascent RNA sequencing data from Drosophila S2 cells...