Repetitive Fragments Research Articles

Utilizing Deep Neural Networks to Fill Gaps in Small Genomes.

With the widespread adoption of next-generation sequencing technologies, the speed and convenience of genome sequencing have significantly improved, and many biological genomes have been sequenced. However, during the assembly of small genomes, we still face a series of challenges, including repetitive fragments, inverted repeats, low sequencing coverage, and the limitations of sequencing technologies. These challenges lead to unknown gaps in small genomes, hindering complete genome assembly. Although there are many existing assembly software options, they do not fully utilize the potential of artificial intelligence technologies, resulting in limited improvement in gap filling. Here, we propose a novel method, DLGapCloser, based on deep learning, aimed at assisting traditional tools in further filling gaps in small genomes. Firstly, we created four datasets based on the original genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Micromonas pusilla. To further extract effective information from the gene sequences, we also added homologous genomes to enrich the datasets. Secondly, we proposed the DGCNet model, which effectively extracts features and learns context from sequences flanking gaps. Addressing issues with early pruning and high memory usage in the Beam Search algorithm, we developed a new prediction algorithm, Wave-Beam Search. This algorithm alternates between expansion and contraction phases, enhancing efficiency and accuracy. Experimental results showed that the Wave-Beam Search algorithm improved the gap-filling performance of assembly tools by 7.35%, 28.57%, 42.85%, and 8.33% on the original results. Finally, we established new gap-filling standards and created and implemented a novel evaluation method. Validation on the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Micromonas pusilla showed that DLGapCloser increased the number of filled gaps by 8.05%, 15.3%, 1.4%, and 7% compared to traditional assembly tools.

Comprehensive analysis of the mitochondrial genome of Ziziphus mauritiana Lam.: Investigating sequence structure, repeat-mediated recombination, chloroplast-derived transfer, RNA editing, and evolution

Ziziphus mauritiana Lam. is a valuable semi-deciduous tropical fruit tree with economic, medicinal, nutritional, and environmental significance. While the chloroplast genome of Z. mauritiana has been studied, the decoding of its mitochondrial genome (mtGenome) is crucial for various research areas, including molecular phylogeny and functional genomics. In this study, we extracted high-quality genomic DNA from the green leaves of Z. mauritiana and assembled the mtGenome by integrating sequencing data from both long and short reads. The Z. mauritiana mtGenome spans 324,124 bp with a 45.43 % GC content and exhibits six distinct conformations alongside the main circular sequence due to three pairs of repetitive fragments that facilitate recombination. RNA editing events resulted in changes in the physicochemical properties of amino acids, with genes expressed at higher levels showing an increased frequency of editing sites. Chloroplast-to-mitochondria horizontal gene transfers occurred in Z. mauritiana; however, these transferred fragments had few mutations, posing a challenge in determining the exact timing of these transfers. Phylogenetic analysis highlights a slower evolution rate of mitochondrial genes compared to chloroplast genes. These insights greatly enhance our understanding of the dynamics of the Z. mauritiana mtGenome, including recombination, gene expression, evolutionary processes, and more. The data and results of this study will serve as valuable mtGenome data resources within the Rhamnaceae family, thereby facilitating further genomics-based studies on Z. mauritiana.

Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences.

Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.

S-o-(p-Methoxyphenylethynyl)benzyl (SMPEB) Glycosides for Catalytic Glycosylation and Their Application in the Synthesis of Polyporus Umbellatus Polysaccharides.

We herein reported a new type of S-o-(p-methoxyphenylethynyl)benzyl donor for a highly efficient glycosylation method. The donor was activated by 10% Tf2O and underwent glycosylation with various acceptors to provide the corresponding glycosides in excellent yield. Furthermore, two repetitive fragments of Polyporus umbellatus polysaccharides (PUPs), isolated from traditional Chinese medicine "Polyporus umbellatus", were prepared by combining the "single-catalyst one-pot" and "latent-active" strategies for the first time for future clear studies on the structure-activity relationship of PUPs.

Fatal toxoplasmosis in a captive squirrel monkey (Saimiri boliviensis) in Portugal

New World monkeys are especially vulnerable to develop severe clinical manifestations and succumb to acute toxoplasmosis. This study aimed to describe the histopathological findings and genotypic characterization of the Toxoplasma gondii strain involved in a lethal case occurring in a zoo-housed black-capped squirrel monkey (Saimiri boliviensis) in Portugal. Cyst-like structures suggestive of Sarcocystidae parasites and acute injuries in liver and brain were observed by light microscopy examination. By immunohistochemistry, calprotectin, T. gondii antigen and Iba1 antigen had a positive signaling in lung, liver and brain tissues. Toxoplasma gondii B1, ITS1 and 529 repetitive element fragments amplifications together with the genotyping of 13 microsatellite markers confirmed a systemic T. gondii infection linked to a non-clonal type II strain. This description is consistent to the majority T. gondii strains circulating in Europe.

Insight into the Organization of the B10v3 Cucumber Genome by Integration of Biological and Bioinformatic Data

The availability of a well-organized and annotated reference genome is essential for genome research and the analysis of re-sequencing approaches. The B10v3 cucumber (Cucumis sativus L.) reference genome has been sequenced and assembled into 8035 contigs, a small fraction of which have been mapped to individual chromosomes. Currently, bioinformatics methods based on comparative homology have made it possible to re-order the sequenced contigs by mapping them to the reference genomes. The B10v3 genome (North-European, Borszczagowski line) was rearranged against the genomes of cucumber 9930 ('Chinese Long' line) and Gy14 (North American line). Furthermore, a better insight into the organization of the B10v3 genome was obtained by integrating the data available in the literature on the assignment of contigs to chromosomes in the B10v3 genome with the results of the bioinformatic analysis. The combination of information on the markers used in the assembly of the B10v3 genome and the results of FISH and DArT-seq experiments confirmed the reliability of the in silico assignment. Approximately 98% of the protein-coding genes within the chromosomes were assigned and a significant proportion of the repetitive fragments in the sequenced B10v3 genome were identified using the RagTag programme. In addition, BLAST analyses provided comparative information between the B10v3 genome and the 9930 and Gy14 data sets. This revealed both similarities and differences in the functional proteins found between the coding sequences region in the genomes. This study contributes to better knowledge and understanding of cucumber genome line B10v3.

Visual and Quantitative Analyses of Virus Genomic Sequences using a Metric-based Algorithm

This work aims to study the virus RNAs using a novel accelerated algorithm to explore any-length repetitive genomic fragments in sequences using Hamming distance between the binary-expressed characters of an RNA and a query pattern. Primary attention is paid to the building and analyzing 1-D distributions (walks) of atg-patterns - codon-starting triplets in genomes. These triplets compose a distributed set called a word scheme of RNA. A complete genome map is built by plotting the mentioned atg-walks, trajectories of separate (a-, c-, g-, and t-symbols) nucleotides, and the lines designating the genomic words. The said map can be additionally equipped by gene’s designations making this tool pertinent for multi-scale genomic analyses. The visual examination of atg-walks is followed by calculating statistical parameters of genomic sequences, including estimating walk- geometry deviation of RNAs and fractal properties of word-length distributions. This approach is applied to the SARS CoV-2, MERS CoV, Dengue, and Ebola viruses, whose complete genomic sequences are taken from GenBank and GISAID. The relative stability of these walks for SARS CoV-2 and MERS CoV viruses was found, unlike the Dengue and Ebola distributions that showed an increased deviation of their geometrical and fractal characteristics. The developed approach can be useful in further studying mutations of viruses and building their phylogenic trees.

Genome-Wide Identification and Characterization of the WRKY Gene Family in Scutellaria baicalensis Georgi under Diverse Abiotic Stress.

The WRKY gene family is an important inducible regulatory factor in plants, which has been extensively studied in many model plants. It has progressively become the focus of investigation for the secondary metabolites of medicinal plants. Currently, there is no systematic analysis of the WRKY gene family in Scutellaria baicalensis Georgi. For this study, a systematic and comprehensive bioinformatics analysis of the WRKY gene family was conducted based on the genomic data of S. baicalensis. A total of 77 WRKY members were identified and 75 were mapped onto nine chromosomes, respectively. Their encoded WRKY proteins could be classified into three subfamilies: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III, based on the characteristics of the amino acid sequences of the WRKY domain and genetic structure. Syntenic analysis revealed that there were 35 pairs of repetitive fragments. Furthermore, the transcriptome data of roots, stems, leaves, and flowers showed that the spatial expression profiles of WRKYs were different. qRT-PCR analysis revealed that 11 stress-related WRKYs exhibited specific expression patterns under diverse treatments. In addition, sub cellular localization analysis indicated that SbWRKY26 and SbWRKY41 were localized in nucleus. This study is the first to report the identification and characterization of the WRKY gene family in S. baicalensis, which is valuable for the further exploration of the biological function of SbWRKYs. It also provides valuable bioinformatics data for S. baicalensis and provides a reference for assessing the medicinal properties of the genus.

ИСТОРИЯ СЮРРЕАЛИСТИЧЕСКОЙ АНТИМУЗЫКАЛЬНОСТИ В ПРАКТИКАХ ИННОВАТИВНОЙ РУССКОЙ ПОЭЗИИ

The article provides an overview of key studies of surrealist musicality, highlights the problem of non-acceptance by surrealism of music media, focuses on a historical discussion of the semantics and reality of sound itself as a phenomenon. It also analyzes the basic principles for the implementation of the surrealist antimusicality in the newest Russian poetry. Anti-musicality is now recognized as the principle of working with sound, bypassing the composer, audial culture, based on ideas about harmony and composition. It is in this anti-musical meaning that the musical code is used in poetic practices of the late 20th century, which destroy the reference narrative and overcome the principles of the classic surrealistic collage. The innovative poetic practice conceptualizes not so much ordered repetitive fragments of a statement as a pause between them, a silence. Such a quantization of aesthetic matter returns reflection to the theoretical horizon of understanding the medium, reduced to its physical foundation in order to further overcome it

Impact of the Heat Transfer Coefficient Determination Method on the Simulation of the Operation of Fin-and-Tube Cross-Flow Heat Exchangers at a Non-Uniform Inflow of Mediums

The work deals with a thermodynamic analysis of finned liquid-gas cross-flow heat exchangers. Analyzing such devices, it is important to determine the heat transfer coefficients on the liquid and the gas side. The analysis basic problem is determination of the of the heat transfer coefficient from the finned surfaces to the flowing gas due to a non-uniform flow of gas through the exchanger. The form and the scope of the gas inflow maldistribution were determined experimentally for two different fins, cross-flow heat exchangers with elliptical tubes. Six Nusselt number correlations were selected and were used to calculate the heat transfer coefficients for measured data. The values of heat transfer coefficient were also computed based on numerical simulations using numerical models of repetitive fragments of the tested heat exchangers. The Wilson plot method was also used. The heat transfer coefficient values were put into an in-house computer code and the experiments were simulated numerically. The comparison of experimental and computational data makes it possible to evaluate different methods of the heat transfer coefficient determination. The simplest Berman correlation for the Nusselt number as well as the computational fluid dynamics based approach gave the best results.

„Lubmy swoje”, czyli o skrzydlatych słowach wywodzących się z piosenek

The present paper discusses winged words having a source in the lyrics of songs written by W. Młynarski and A. Osiecka. The article also contains examples of such units derived from the texts of other authors, including J. Przybora. The authors chose winged words having their source in the song, because this genre has a strong impact on the Polish language. There are recorded in Polish language, first of all, song titles, repetitive fragments, first of all parts of their choruses. Repeatability of the word relationship in the song favors its recording. In addition to the canonical forms of the analyzed word combinations, for example: W co się bawić; Róbmy swoje; Niech żyje bal! czy Jak dobrze mieć sąsiada, the authors also discuss their various modifications, for example: Lubmy swoje; Jak dobrze znać swojego sąsiada; Jak dobrze mieć tatę. In their considerations, the authors refer to the study of winged words conducted by A. M. Lewicki, W. Chlebda, J. Tarsa and J. Ignatowicz-Skowrońska.

Immune reactivity to Trypanosoma cruzi chimeric proteins for Chagas disease diagnosis in immigrants living in a non-endemic setting

BackgroundChronic Chagas Disease (CD) diagnosis is based on serological methods employing crude, semipurified or recombinant antigens, which may result in low sensitivity or cross-reactivity. To reduce these restrictions, we developed a strategy involving use of molecules containing repetitive fragments of Trypanosoma cruzi conserved proteins. Diagnostic performance of IBMP-8.1 and IBMP-8.4 chimeric antigens (Molecular Biology Institute of Paraná - IBMP in Portuguese acronym) was assessed to diagnose T. cruzi-infected and non-infected immigrants living in Barcelona (Spain), a non-endemic setting for Chagas disease.MethodsReactivity of IBMP-8.1 and IBMP-8.4 was assessed using an in-house automated ELISA with 347 positive and 331 negative individuals to Chagas disease. Antigenic cross-reactivity was measured with sera samples from pregnant women with Toxoplasma gondii (n = 98) and Zika virus (n = 75) antibodies.ResultsThe area under the curve values was 1 and 0.99 for the IBMP-8.1 and IBMP-8.4 proteins, respectively, demonstrating excellent diagnostic accuracy. The reactivity index was higher for IBMP-8.1 than IBMP-8.4 in positive samples and no significant difference in reactivity index was observed in negative samples. Sensitivity ranged from 99.4% for IBMP-8.1 to 99.1% for IBMP-8.4 and was not statistically different. Specificity for IBMP-8.1 reached 100 and 99.7% for IBMP-8.4, both nearly 100% accurate. No antigenic cross-reactivity was observed and reactivity index was similar to that for negative Chagas disease individuals.ConclusionsOur results showed an outstanding performance of IBMP-8.1 and IBMP-8.4 chimeric antigens by ELISA and suggest both chimeric antigens could also be used for Chagas disease diagnosis in immigrants living in non-endemic settings.

Branched DNA Junction-Enhanced Isothermal Circular Strand Displacement Polymerization for Intracellular Imaging of MicroRNAs.

The microRNA profiles within living cells are informative for diagnosis and prognosis of human cancers. In the present work, we developed a new sensing strategy based on branched DNA junction-enhanced isothermal circular strand displacement polymerization (B-ICSDP) for the detection and intracellular imaging of microRNAs in living cells of interest. A circular DNA template consisting of three repetitive fragments serves as the scaffold for the self-assembly of sophisticated signaling probes, resulting a shrunk branched DNA junction. Target microRNA triggers the opening of molecular beacon, not only restoring the quenched fluorescence but also activating a circular polymerization-based strand displacement reaction. Thus, patulous branched DNA junction is abundantly formed, generating the amplified signal. It is noteworthy that great heaps of branched product assemblies can be also achieved in living cells, and the intracellular enzymatic assembly based strategy is able to be used to recognize specific microRNA-expressed cancer cells. Moreover, different microRNAs coexisting in the same living cells can be simultaneously screened without any interference from each other by confocal laser scanning microscopy. The measured data from confocal fluorescence imaging of different cancer cells demonstrates that the B-ICSDP-based system is a promising alternative for in vivo analysis of microRNAs in complicated biological samples.

On the origin of crystallinity: a lower bound for the regularity radius of Delone sets.

The mathematical conditions for the origin of long-range order or crystallinity in ideal crystals are one of the very fundamental problems of modern crystallography. It is widely believed that the (global) regularity of crystals is a consequence of `local order', in particular the repetition of local fragments, but the exact mathematical theory of this phenomenon is poorly known. In particular, most mathematical models for quasicrystals, for example Penrose tiling, have repetitive local fragments, but are not (globally) regular. The universal abstract models of any atomic arrangements are Delone sets, which are uniformly distributed discrete point sets in Euclidean d space. An ideal crystal is a regular or multi-regular system, that is, a Delone set, which is the orbit of a single point or finitely many points under a crystallographic group of isometries. The local theory of regular or multi-regular systems aims at finding sufficient local conditions for a Delone set X to be a regular or multi-regular system. One of the main goals is to estimate the regularity radius \hat{\rho}_d for Delone sets X in terms of the radius R of the largest `empty ball' for X. The celebrated `local criterion for regular systems' provides an upper bound for \hat{\rho_d} for any d. Better upper bounds are known for d ≤ 3. The present article establishes the lower bound \hat{\rho_d}\geq 2dR for all d, which is linear in d. The best previously known lower bound had been \hat{\rho}_d\geq 4R for d ≥ 2. The proof of the new lower bound is accomplished through explicit constructions of Delone sets with mutually equivalent (2dR - ℇ)-clusters, which are not regular systems. The two- and three-dimensional constructions are illustrated by examples. In addition to its fundamental importance, the obtained result is also relevant for the understanding of geometrical conditions of the formation of ordered and disordered arrangements in polytypic materials.

Repetitive Right Dislocation Constructions and Repetitive Fragments: With Reference to Verbal Idioms in Korean

The idiomatically combining expressions (ICEs) are compositional. In the repetitive right dislocation constructions (RDCs), the ICE correlate is identical with the ICE appendix, which is fronted in the appendix clause, followed by clausal ellipsis. The present work introduces the repetitive fragment answer, which is fronted to the sentence-initial position (i.e., Spec-CP) to be focused, followed by clausal ellipsis, keeping its idiomatic meaning unharmed. In the case of the repetitive fragment answer, the function of the focusing adverb modifying the verbal idiom including correlate in the direct (wh-)question is to put a strong emphasis on the correlate and induces the fragment answer to be focused. There is parallelism between the repetitive ICE RDCs and their corresponding repetitive ICE fragment answers in Korean, which shows that a natural consequence under the standard assumption that fragments are derived by ellipsis and are island-insensitive due to the repair effect.

Pendant/bridged/mesoporous silsesquioxane nanoparticles: Versatile and biocompatible platforms for smart delivery of therapeutics

Silsesquioxane nanoparticles are composed of repetitive organosilica fragments in their frameworks and are now recognized to have outstanding functional fertility. Depending on the organosilane and the synthetic pathways, silsesquioxane NPs can be pendant, bridged, dense or porous. Recently the diverse functionalities of mesoporous silsesquioxane nanoparticles have been exploited for the sake of drug-related biomedicine. Fine-tuning the silsesquioxane nanoparticles characteristics allow not only a superior retention capacity of therapeutics without the need of any further modification, but also a controlled release through various environmentally-stimulated triggers. The main focus of the present review is to highlight the different types of silsesquioxane nanoparticles and their exceptional features focused on controlled delivery of drugs, proteins, antibodies and DNA through pH, redox or light stimuli.

Identification of Potential Reusable Subroutines in Recorded Automated Test Scripts

In the automated testing based on actions in user interface of the tested application, one of the key challenges is maintenance of these tests. The maintenance overhead can be decreased by suitably structuring the test scripts, typically by employing reusable objects. To aid in the development, maintenance and refactoring of these test scripts, potentially reusable objects can be identified by a semi-automated process. In this paper, we propose a solution that identifies the potentially reusable objects in a set of automated test scripts and then provides developers with suggestions about these objects. During this process, we analyze the semantics of specific test steps using a system of abstract signatures. The solution can be used to identify the potentially reusable objects in both recorded automated test sets and tests programmed in an unstructured style. Moreover, compared to approaches that are based solely on searching for repetitive source code fragments, the proposed system identifies potentially reusable objects that are more relevant for test automation.

A Novel Combination of Percutaneous Endoscopic Lumbar Discectomy and Epiduroscopic Laser Neural Decompression for Down-migrated Disc Herniation

Although percutaneous endoscopic lumbar discectomy (PELD) is an effective treatment for herniated discs, its application in a disc with extensive migration is still challenging. As such, epiduroscopic laser neural decompression (ELND) provides a new view of the epidural space as well as an alternative treatment for a herniated disc and epidural fibrosis. In this paper the authors introduce the novel combination of PELD and ELND for high grade down-migrated disc herniation. An 87-year old woman presented with severe pain radiating down her leg due to high grade down-migrated disc herniation at L4-5. The therapeutic plan was organized into 3 steps. First, the patient underwent PELD to remove the paracentral extruded disc and open the epidural space between the traversing nerve root and disc space. Second, ELND was performed to remove the down-migrated disc and simultaneously push the free fragment to the L4-5 disc space. Lastly, repetitive free fragments were picked up and streamed upward using ELND. The patient reported significant reduction of pain after surgery. Postoperative magnetic resonance imaging (MRI) showed complete removal of the ruptured disc fragment. A combination of PELD and ELND may be an option of treatments for down-migrated disc herniation. Key words: Percutaneous endoscopic lumbar discectomy, epiduroscopic laser neural decompression, down-migrated disc herniation

The Variable Markov Oracle: Algorithms for Human Gesture Applications

This article introduces the Variable Markov Oracle (VMO) data structure for multivariate time series indexing. VMO can identify repetitive fragments and find sequential similarities between observations. VMO can also be viewed as a combination of online clustering algorithms with variable-order Markov constraints. The authors use VMO for gesture query-by-content and gesture following. A probabilistic interpretation of the VMO query-matching algorithm is proposed to find an analogy to the inference problem in a hidden Markov model (HMM). This probabilistic interpretation extends VMO to be not only a data structure but also a model for time series. Query-by-content experiments were conducted on a gesture database that was recorded using a Kinect 3D camera, showing state-of-the-art performance. The query-by-content experiments' results are compared to previous works using HMM and dynamic time warping. Gesture following is described in the context of an interactive dance environment that aims to integrate human movements with computer-generated graphics to create an augmented reality performance.

Large tandem repeats of Mesocricetus auratus in silico and in situ

The class of tandemly repeated sequences exists only in eukaryotic genomes and absent in prokaryotes. The tens percent of eukaryotic genome are built up of the tandem repeats. The whole set of different tandem repeats is not revealed to any of the eukaryote species in spite of the half century history of its investigation by molecular biology methods. Previously we found the set of tandem repeats in the database of well assembled mouse genome with the bioinformatics methods. In the current work we applied the same methods to the poorly assembled hamster Mesocricetus auratus genome. 19 tandem repeats families have been found in hamster genome by bioinformatics (in silico). Only one of tandem repeats' families found have been cloned previously and exists in the Repbase, the database of all known repetitive fragments. The rest of the families are new and need the experimental verification by FISH (in situ). Oligo probes were designed at the base of in silico found sequences. Oligo probe for the known tandem repeat gives the same signal as the cloned probe, i.e., probes designed are suitable for oligo-FISH. All four oligo probes tested give signal at the heterochromatic centromeric region as expected, though with different intensities and at different number of chromosomes. The results show the power of the in silico methods for the mostly mysterious genome component, tandem repeats, investigation.