Splicing System Research Articles

Virtual Roaming of Cultural Heritage Based on Image Processing

ABSTRACTWith the digital protection and development of cultural heritage as a focus, an analysis of the trends in cultural heritage digitization reveals the importance of digital technology in this field, as demonstrated by the application of virtual reality (VR) to the protection and development of the Lingjiatan site. The implementation of the Lingjiatan roaming system involves sequential steps, including image acquisition, image splicing, and roaming system production. A user test was conducted to evaluate the usability and user experience of the system. The results show that the system operates normally, with smooth interactive functions that allow users to tour the Lingjiatan site virtually. Users can learn about Lingjiatan's culture from this virtual environment. This study further explores the system's potential for site preservation and development, and its role in the integration of cultural heritage and tourism.

Spectral Bipartition via Gap Cut on DNA Sequences

Deoxyribonucleic Acid (DNA) and graph partitioning are two distinct fields of study which can be linked in the structure of biological networks. Graph partitioning has been extensively studied but not its application in the biological field. This research explored on the application of spectral graph partitioning in DNA splicing, aiming to simulate the cleavage of DNA by performing spectral bipartition on DNA sequences in a DNA splicing system. This research incorporates Fiedler theory and algebraic graph theory, which are commonly utilized in network analysis and the analysis of graph connectivity. Some DNA sequences of even length are selected and expressed in graphical representations. The adjacency matrix, Laplacian matrix, and degree matrix are computed from the graphs, as well as the Fiedler value and Fiedler vector associated with the graphs. Gap cut is used as a method of spectral bipartition which produces two partitions of DNA sequence of unequal lengths. The generalizations of gap cut on DNA sequences of even length are provided as lemmas and theorem.

Monolithic linear array fiber end cap for spectral beam combination

In this study, a fusion splicing system that facilitates the splicing of a monolithic linear array fiber end cap is constructed. The fusion splicing thermal field of the end cap irradiated by a CO2 laser is theoretically simulated using the finite element method. The experimental fusion splicing temperature agrees well with the simulation results. The splicing strength, misalignment, and high-power withstanding capacity of the fusion-spliced monolithic linear 3-fiber end cap are investigated. The use of the fabricated device in a dual-grating spectral beam combination (SBC) is also demonstrated with three-channel laser beams, achieving a combined beam with near-diffraction-limited beam quality M2=1.101. It shows that the development of the monolithic linear array fiber end cap is meaningful for achieving a compact high-brightness SBC system.

Ultrasonic Control of Protein Splicing by Split Inteins.

Utilizing ultrasound as an external stimulus to remotely modulate the activity of proteins is an important aspect of sonopharmacology and establishes the basis for the emerging field of sonogenetics. Here, we describe an ultrasound-responsive protein splicing system that enables spatiotemporal control of split-intein-mediated protein ligation. The system utilizes engineered split inteins that are caged and can be activated by thrombin released from a high molar mass DNA-based carrier under focused ultrasound sonication. This approach represents a general method for controlling the functions of proteins of interest by ultrasound, as demonstrated here by the controlled synthesis of the superfolder green fluorescence protein (GFP) and calcitonin. Furthermore, calcitonin receptor-mediated signal transduction in cells was triggered by this system in vitro without harming cell viability. By expanding the sonogenetic toolbox with protein splicing technologies, this study provides a possible pathway to deploy ultrasound for remotely controlling a variety of protein functions in deep tissue in the future.

A compact, versatile drug-induced splicing switch system with minimal background expression

Gene-switch techniques hold promising applications in contemporary genetics research, particularly in disease treatment and genetic engineering. Here, we developed a compact drug-induced splicing system that maintains low background using a human ubiquitin C (hUBC) promoter and optimized drug (LMI070) binding sequences based on the Xon switch system. To ensure precise subcellular localization of the protein of interest (POI), we inserted a 2A self-cleaving peptide between the extra N-terminal peptide and POI. This streamlined and optimized switch system, named miniXon2G, effectively regulated POIs in different subcellular localizations both invitro and invivo. Furthermore, miniXon2G could be integrated into endogenous gene loci, resulting in precise, reversible regulation of target genes by both endogenous regulators and drugs. Overall, these findings highlight the performance of miniXon2G in controlling protein expression with great potential for general applicability to diverse biological scenarios requiring precise and delicate regulation.

Whole paternal uniparental disomy of chromosome 4 with a novel homozygous IDUA splicing variant, c.159-9T>A, in a Chinese patient with mucopolysaccharidosis type I.

Mucopolysaccharidosis type I (MPS-I) is a rare autosomal recessive genetic lysosomal storage disorder that is caused by pathogenic variants of the α-L-iduronidase (IDUA) gene. This study aimed to identify the genetic causes of MPS-I in a Chinese patient and construct a minigene of IDUA to analyze its variants upon splicing. Whole-exome sequencing (WES) and Sanger sequencing were used to confirm the potential causative variants. Single-nucleotide polymorphism (SNP) array was subsequently performed to confirm uniparental disomy (UPD). Minigene assay was performed to analyze the effect on splicing of mRNA. We meanwhile explored the conservative analysis and protein homology simulation. A novel homozygous splicing mutation of IDUA, c.159-9T>A, was identified in an individual presenting with overlapping features of MPS-I. Interestingly, only the father and sisters, but not the mother, carried the variant in a heterozygous state. WES and SNP array analyses validated paternal UPD on chromosome 4. Minigene splicing revealed two aberrant splicing events: exon 2 skipping and intron 1 retention. Moreover, the specific structure of the mutant protein obviously changed according to the results of the homologous model. This study describes a rare autosomal recessive disorder with paternal UPD of chromosome 4 leading to the homozygosity of the IDUA splicing variant in patients with MPS-I for the first time. This study expands the variant spectrum of IDUA and provides insights into the splicing system, facilitating its enhanced diagnosis and treatment.

The Generalisations of n-Cutting Sites Splicing Languages via Yusof-Goode Splicing System using a Non-Palindromic Rule and Crossing Site

Yusof-Goode (Y-G) splicing system was introduced in the context of Formal Language Theory. Splicing system is a dry model that presents enzymatic activities between initial strings and restriction enzymes, while splicing language is the generated strings from the splicing system. Splicing language will yield either as new molecules or initial string itself, and can be either in adult or inert, limit or transient languages. In this paper, some mathematical results on generating and generalising the n-cutting sites splicing languages are established using a Y-G splicing system consisting of a single pattern of strings with non-palindromic rule and crossing site. Two lemmas are presented to discuss the Y-G splicing system when two and three cutting sites exist in a single pattern of string. Different characteristics concerning the features of left and right contexts are established. A theorem is then proposed based on the lemmas to generalise the n-cutting sites splicing languages resulting from a Y-G splicing system with a single pattern of string and a non-palindromic rule when n-cutting sites exist in a single pattern of string.

Characterize Type of Splicing Languages via Directed Splicing Graph

A splicing system is a formal characterization of the ability to generate certain enzymatic activities acting on deoxyribonucleic acid (DNA) molecules. In this paper, the results from Laun’s experiment are used in characterizing the type of splicing languages. In the experiments, two initial strings are involved with different features on the selected restriction enzymes. Case I and Case II discussed in this paper show that the splicing languages obtained from these experiments are in adult and limit languages. Nevertheless, the result obtained in this paper is more precise in showing the type of splicing languages which is beyond adult and limit languages when presented via a directed splicing graph. The features of the restriction enzyme that affect the formation of active persistent language are investigated based on the results proposed by Yusof.

A Bibliometric Review on Deoxyribonucleic Acid (DNA) Splicing System

This study objects to provide a communicative review for splicing system, focusing on deoxyribonucleic acid (DNA) published in journals and proceedings indexed by the Scopus database. The method of bibliometric analysis is used to describe and analyze the evolution of publication structure and its various co-relationships such as citation, co-citation, co-authorship, and co-occurrence, among the chosen 174 documents indexed by Scopus. This study gives some insightful direction of research where the most influential documents and authors were determined. Besides, the emerging of technologies in most of the research works conducted previously promote the hybridization of background of studies specifically in mathematics, biology, and computer science. The study is limited to English articles which was published by the Scopus database, ranging from the year of 1983 until 2023. The source is also limited to Scopus journals and proceedings only. As far as the authors are aware, this is the first study to address the splicing system topic from a bibliometric perspective. The authors believe that this bibliometric review will help scholars and researchers to stand firm bases regarding the scientific development of this field of study.

Classification of n-th Order Limit Language in Formal Language Classes

The study of splicing systems and their language has grown rapidly since Paun developed a splicing system known as a regular splicing scheme that produces a regular language. Since then, the researchers have been eager to classify the splicing language into certain classes in the Chomsky hierarchy, such as context-free language, context-sensitive language and recursive enumerable language. Previously, the study on the n-th order limit language was conducted from the biological perspective to the limit language produced. Still, no research has been done from the generation of language point of view. This research presents a generalization on the type of classes of the formal language, the n-th order limit language. The cases to obtain the n-th order limit language are revisited and used to obtain the types of language classes according to the Chomsky hierarchy produced by the n-th order limit language.

Conditional splicing system for tight control of viral overlapping genes.

Regulating overlapping genes is vital for gene therapy and vaccine development using viral vectors. The regulation of overlapping genes presents challenges, including cytotoxicity and impacts on vector capacity and genome stability, which restrict stable packaging cell line development and broad application. To address these challenges, we present a "loxp-splice-loxp"-based conditional splicing system, offering a novel solution for conditional expression of overlapping genes and stable cell line establishment. This system may also regulate other cytotoxic genes, representing a significant advancement in cell engineering and gene therapy as well as biomass production.

Ultra-High-Performance Concrete (UHPC) Piles and Splicing Options

Conventional driven piles are made from steel, concrete, timber, or composite materials. These piling options have limitations with respect to corrosion, durability, driveablity, and performance. Ultra-High-Performance Concrete (UHPC) pile is a new alternative that has already been adopted by various state Departments of Transportation in the United States for addressing the limitations that exist with conventional piles. UHPC piles are made of a cementitious composite material mixture that possesses exceptional properties such as higher strength, low capillary porosity, and high resistance to corrosion, making them a suitable option for use as a deep foundation. For several reasons, it is necessary to cast piles with a shorter length and splice them at the site to reach the desired lengths. These reasons include shipping limitations, unpredictable soil condition, reducing transportation costs, construction time, and damage during installation. This study aims to explore and summarize the currently available options for connecting UHPC pile segments. Accordingly, after a brief introduction on driven piles, this paper investigates various splicing systems that can be used for UHPC piles through reviewing previous research studies and field applications. The applicable splices are then compared based on several criteria such as capacity, durability, cost, and ease of application.

Hypertrophic cardiomyopathy in MYBPC3 carriers in aging.

Hypertrophic cardiomyopathy (HCM) is characterized by abnormal thickening of the myocardium, leading to arrhythmias, heart failure, and elevated risk of sudden cardiac death, particularly among the young. This inherited disease is predominantly caused by mutations in sarcomeric genes, among which those in the cardiac myosin binding protein-C3 (MYBPC3) gene are major contributors. HCM associated with MYBPC3 mutations usually presents in the elderly and ranges from asymptomatic to symptomatic forms, affecting numerous cardiac functions and presenting significant health risks with a spectrum of clinical manifestations. Regulation of MYBPC3 expression involves various transcriptional and translational mechanisms, yet the destiny of mutant MYBPC3 mRNA and protein in late-onset HCM remains unclear. Pathogenesis related to MYBPC3 mutations includes nonsense-mediated decay, alternative splicing, and ubiquitin-proteasome system events, leading to allelic imbalance and haploinsufficiency. Aging further exacerbates the severity of HCM in carriers of MYBPC3 mutations. Advancements in high-throughput omics techniques have identified crucial molecular events and regulatory disruptions in cardiomyocytes expressing MYBPC3 variants. This review assesses the pathogenic mechanisms that promote late-onset HCM through the lens of transcriptional, post-transcriptional, and post-translational modulation of MYBPC3, underscoring its significance in HCM across carriers. The review also evaluates the influence of aging on these processes and MYBPC3 levels during HCM pathogenesis in the elderly. While pinpointing targets for novel medical interventions to conserve cardiac function remains challenging, the emergence of personalized omics offers promising avenues for future HCM treatments, particularly for late-onset cases.

Various fiber optic microlenses fabricated using a large diameter splicing system

We developed and fabricated various types of microlenses on optical fiber end facets using a large diameter splicing (LDS) system and analyzed the obtained beam profiles. Numerical simulations support our experimental results.

Counting subwords in circular words and their Parikh matrices

The word inference problem is to determine languages such that the information on the number of occurrences of those subwords in the language can uniquely identify a word. A considerable amount of work has been done on this problem, but the same cannot be said for circular words despite growing interests on the latter due to their applications—for example, in splicing systems. Meanwhile, Parikh matrices are useful tools and well established in the study of subword occurrences. In this work, we propose two ways of counting subword occurrences in circular words. We then extend the idea of Parikh matrices to the context of circular words and investigate this extension. Motivated by the word inference problem, we study ambiguity in the identification of a circular word by its Parikh matrix. Accordingly, two rewriting rules are developed to generate ternary circular words which share the same Parikh matrix.

Structural insights into intron catalysis and dynamics during splicing

The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns1,2. Despite the importance of branching in RNA metabolism, structural understanding of this process has remained elusive. Here we present a comprehensive analysis of three single-particle cryogenic electron microscopy structures captured along the splicing pathway. They reveal the network of molecular interactions that specifies the branchpoint adenosine and positions key functional groups to catalyse lariat formation and coordinate exon ligation. The structures also reveal conformational rearrangements of the branch helix and the mechanism of splice site exchange that facilitate the transition from branching to ligation. These findings shed light on the evolution of splicing and highlight the conservation of structural components, catalytic mechanism and dynamical strategies retained through time in premessenger RNA splicing machines.

Nilai Sosial Masyarakat Samin di Desa Larikrejo Undaan Kudus

This study discusses the social values ??of the Samin people in the village of Larikrejo which aims to (1) find out the factors that cause the Samin people to stick to their values ??and traditions, (2) find out the social values ??of the Samin tribe and (3) find out the values ??and the traditions of the Samin people in terms of everyday life. In this study, researchers used ethnographic research methods. The ethnographic method is a method used to describe things related to the Samin community in depth. In this study, it shows that social values ??between the Samin people and the surrounding community are in the form of cooperation and interaction, this form of interaction, both the Samin tribe and the community in general, often cooperate in terms of mutual cooperation between members of the community, for example mutual cooperation in building residents' houses in splice system. In social interaction between the Samin community and the surrounding community, it is influenced by several factors, namely the social situation, the power of group norms, personal goals, position and individual conditions and finding situations. The obstacles faced in social interaction between the Samin community and the surrounding community are language differences that are difficult for the surrounding community to understand and the difference in values ??between the two social groups.

The novel compound heterozygous variants identified in a Chinese family with glucose phosphate isomerase deficiency and pathogenicity analysis

Background and Aims:Glucose phosphate isomerase (GPI) deficiency is an extremely rare autosomal recessive disorder caused by mutations in the GPI gene. In this research, the proband displaying typical manifestations of haemolytic anaemia and his family members were recruited to analyse the pathogenicity of the detected variants.Methods:Peripheral blood samples were collected from the family members and genomic DNA was extracted and targeted for capture and sequencing. The effect of the candidate pathogenic variants on splicing was further investigated using the minigene splicing system. The computer simulation was also used for further analysis of the detected data.Results:The proband carried the compound heterozygous variants c.633 + 3 A > G and c.295G > T in the GPI gene, which have never been reported before. In the genealogy, co-segregation of the mutant genotype with the phenotype was established. The minigene study showed that intronic mutations resulted in abnormal pre-mRNA splicing. Specifically, the two aberrant transcripts: r.546_633del and r.633 + 1_633 + 2insGT were transcribed by the minigene plasmid expressing the c.633 + 3 A > G variant. The missense mutation c.295G > T in exon 3 resulted in altering glycine at codon 87 to cysteine which was predicted to be pathogenic in an in silico analysis. Deeper analyses revealed that the Gly87Cys missense mutation led to steric hindrance. Compared to the wild-type, the mutation G87C led to a significant increase in intermolecular forces.Conclusion:Overall, the novel compound heterozygous variants in the GPI gene contributed to the etiology of the disease. Genetic testing can assist in the diagnosis. The novel gene variants identified in the present study has further expanded the mutational spectrum of GPI deficiency, which can better guide family counselling.

Molecular evidence for the involvement of alternative splicing in jejunum epithelial cells in broiler chickens fed dietary supplementation with olive mill wastewater.

There is no doubt that alternative splicing is conserved in chickens and mammals, but evaluating the effects of nutrition on alternative splicing in chickens is crucial in a wide range of fields. Although the olive diet has been extensively studied in human, mouse, and chicken systems, little is known about its impact on chicken alternative splicing systems. Hence, the current study aimed to assess the effect of feeding polyphenol-enriched olive mill wastewater to female broiler chickens via alternative splicing by analyzing high-throughput sequencing raw reads of RNA utilizing genomics and bioinformatics methodologies. It also aimed to look for differences in isoform expression and discover molecular functions and biological processes linked to differentially transcribed genes. The findings of our study revealed that 51 genes involved in isoform switching and alternative splicing events were not used evenly. This is due to the reduced use of ATSS in olive mill wastewater groups compared to control groups. Furthermore, the gene ontology analysis revealed that 25 GO terms were enriched in biological processes, 16 GO terms were enriched in molecular function, and 25 GO terms were enriched in cellular components. Kinase and adenylyltransferase activities were significantly enriched in terms. The molecular analysis presented herein provides valuable insight into the role of phenolics in alternative gene-splicing mechanisms in chickens, demonstrating how an industrial waste product can be repurposed as a feed supplement with a satisfactory outcome.

A Review: Restricted Splicing Systems

In 1987, Head [1] proposed a splicing method as a mathematical model for DNA recombination. In this model, two DNA molecules are cut at specific recognition sites, and the prefix of one molecule is combined with the suffix of the other, creating a new string. Splicing operations in the system are represented as splicing rules, formalizing the process as a string operation. By iteratively applying a set of splicing rules to a set of initial strings or axioms, a language can be generated, which is known as a splicing language. According to the Chomsky hierarchy, these languages are classified as regular languages, the lowest level of language. To enhance the generative power of splicing languages, restrictions are introduced. This research reviews three splicing system restrictions: weighted splicing [2], group splicing [3], and probabilistic splicing [4].