Assembly Program Research Articles

Stepwise virus assembly in the cell nucleus revealed by spatiotemporal click chemistry of DNA replication.

Biomolecular assemblies are fundamental to life and viral disease. The spatiotemporal coordination of viral replication and assembly is largely unknown. Here, we developed a dual-color click chemistry procedure for imaging adenovirus DNA (vDNA) replication in the cell nucleus. Late- but not early-replicated vDNA was packaged into virions. Early-replicated vDNA segregated from the viral replication compartment (VRC). Single object tracking, superresolution microscopy, fluorescence recovery after photobleaching, and correlative light-electron microscopy revealed a stepwise assembly program involving vDNA and capsid intermediates. Depending on replication and the scaffolding protein 52K, late-replicated vDNA with rapidly exchanging green fluorescent protein-tagged capsid linchpin protein V and incomplete virions emerged from the VRC periphery. These nanogel-like puncta exhibited restricted movements and were located with the capsid proteins hexon, VI, and virions in the nuclear periphery, suggestive of sites for virion formation. Our findings identify VRC dynamics and assembly intermediates, essential for stepwise productive adenovirus morphogenesis.

Reexamining the Mycovirome of Botrytis spp.

Botrytis species cause gray mold disease in more than 200 crops worldwide. To control this disease, chemical fungicides are usually applied. However, more sustainable control alternatives should be explored, such as the use of hypovirulent mycovirus-infected fungal strains. To determine the mycovirome of two Botrytis species, B. cinerea and B. prunorum, we reanalyzed RNA-Seq and small RNA-Seq data using different assembly programs and an updated viral database, aiming to identify new mycoviruses that were previously not described in the same dataset. New mycoviruses were identified, including those previously reported to infect or be associated with B. cinerea and Plasmopara viticola, such as Botrytis cinerea alpha-like virus 1 and Plasmopara viticola lesion-associated ourmia-like virus 80. Additionally, two novel narnaviruses, not previously identified infecting Botrytis species, have been characterized, tentatively named Botrytis cinerea narnavirus 1 and Botrytis narnavirus 1. The analysis of small RNAs suggested that all identified mycoviruses were targeted by the antiviral fungal mechanism, regardless of the viral genome type. In conclusion, the enlarged list of newly found viruses and the application of different bioinformatics approaches have enabled the identification of novel mycoviruses not previously described in Botrytis species, expanding the already extensive list.

Pitching the Tent: Understanding the Arctic Circle 2013–2023

ABSTRACT The aim of this article is to examine in greater detail the Arctic Circle at the end of its first decade. Gaining more and better insight into the Arctic Circle’s own roles and significance is not just a useful contribution in its own right, but is also likely to shed fresh light on the Arctic conferencing and Arctic governance academic literature. Through an analysis of Arctic Circle assembly programmes and other materials, it is argued here that the Arctic Circle has emerged playing a multidimensional role on the world stage. Thus, the Arctic Circle’s importance is best understood from a range of different perspectives, the most apparent of which are articulated and discussed here.

RANCANG BANGUN PROTOTYPE SMART GREENHOUSE MENGGUNAKAN THINGSPEAK

The design of this smart greenhouse prototype is one of the implementations of artificial intelligence controlled by the Arduino uno microcontroller, which has actuators in the form of lights and pumps and is equipped with DHT22 sensors, Soil Moisture and Temperature Sensors. The method used in making this smart greenhouse prototype is the Prototype method. There are seven stages in the prototype method that guide the process of making robots, namely gathering requirements, building prototypes/prototypes, evaluating prototypes, programming systems, testing systems, evaluating systems, and using the system. The most important stage in making this smart greenhouse prototype is the stage where at this stage testing is carried out on the results of the design and programming of the robot that has been made to prove the robot prototype is in accordance with what is desired or not. The testing process is carried out in tandem with the assembly process and programming process. In the process of assembling and programming the robot prototype, it is done with system errors. Testing with system errors is carried out to get a robot prototype that works optimally.

JAVA BASED FIRST-PERSON SHOOTER (FPS) GAME WITH REMASTERED GRAPHICS

Our project aims to accurately examine an old game's assembly source, comprehend its usefulness, and convert it into efficient Java code. Using Java's object-oriented characteristics, the emphasis is on restructuring and organizing code to make it more maintainable and comprehensible. The successful conversion of this game to Java demonstrates how knowledge of low-level assembly programming can supplement skill in high-level Java programming, resulting in a smooth integration of traditional gameplay with current technology. This integration not only heightens perceptions but also makes the game more accessible to modern audiences, providing an immersive gaming experience that combines the game's original character with contemporary software development standards. The enhanced graphics will also include upgrading game elements including textures, models, and special effects. The enhanced graphics will include improved game assets like textures, models, and special effects, as well as advanced lighting and shading effects. In addition, the game's user interface will be updated to increase use and appearance. The project's goal is to demonstrate the integration of classic FPS gameplay with contemporary graphics technology, providing players with an enhanced gaming experience that combines the recollections of old FPS games with the visual quality of modern gaming. Key Words: - Java programming, game development , FPS game, graphics.

THE DESIGN OF THE PIPELINED RISC-V PROCESSOR WITH THE HARDWARE COPROCESSOR OF DIGITAL SIGNAL PROCESSING

Context. The digital signal processing is applied in many fields of science, technology and human activity. One of the ways of implementing algorithms of digital signal processing is the development of coprocessors as an integral part of well-known architectures.
 In the case of developing a pipelined device, the presented approach will allow to use software and hardware tools of the appropriate architecture, provide the faster execution of signal processing algorithms, reduce the number of cycles and memory accesses.
 Objective. Objectives are design and characterization study of a pipelined RISC-V processor and coprocessor of digital signal processing which performs fast Fourier transform.
 Method. Analyzing technical literature and existing decisions allow to assess advantages and disadvantages of modern developments and on the basis of which to form the relevance of the selected topic. Model designing and simulation results allow to examine a model efficiency, to determine weak components’ parts and to improve model parameters.
 Results. The pipelined RISC-V processor has been designed which executes a basic set of instructions. Execution time of assembly program on the single-cycled and the pipelined processors have been analyzed. According to the results, the test program on the pipelined processor is executed in 29 cycles, while on the single-cycle processor it takes 60 cycles. The structure of the coprocessor for the fast Fourier transform algorithm and a set of processor instructions that allow working with the coprocessor have been developed. The number of cycles of the coprocessor based on Radix-2 fast Fourier transform algorithm for 512 points is 2358 cycles, and for 1024 points is 5180 cycles.
 Conclusions. Conducted researches and calculations have showed that the application of the developed hardware coprocessor reduces the fast Fourier transform algorithm execution time and the load of the pipelined processor during calculations.

DEGAP: Dynamic elongation of a genome assembly path.

Genome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembly software programs and algorithms, it is still a great challenge to assemble a complete genome without any gaps. With the latest DNA circular consensus sequencing (CCS) technology, several assembly programs can now build a genome from raw sequencing data to contigs; however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software, DEGAP (Dynamic Elongation of a Genome Assembly Path), that resolves gap regions by utilizing the dual advantages of accuracy and length of high-fidelity (HiFi) reads. DEGAP identifies differences between reads and provides 'GapFiller' or 'CtgLinker' modes to eliminate or shorten gaps in genomes. DEGAP adopts an iterative elongation strategy that automatically and dynamically adjusts parameters according to three complexity factors affecting the genome to determine the optimal extension path. DEGAP has already been successfully applied to decipher complex genomic regions in several projects and may be widely employed to generate more gap-free genomes.

An Efficient Reduction of Timer Interrupts for Model Checking of Embedded Assembly Programs

In verifying programs for embedded systems, it is essential to reduce the verification time because state explosion may occur during model checking. One solution is to reduce the number of interrupt handler executions. In particular, when periodic interrupts such as timer interrupts are incorporated, it is necessary to know the physical time. In this paper, we define a control flow automaton (CFA) that can handle time and propose an algorithm based on interrupt handler execution reduction (IHER). The proposed method reduces the number of interrupt executions, including timer interrupts. A case study verified the effectiveness of this algorithm.

RFGR: Repeat Finder for Complete and Assembled Whole Genomes and NGS Reads.

Repetitive DNA sequences cause genomic instability and are important genetic markers. Identification of repeats is a critical step in genome annotation and analysis. On the other hand, repeats also pose a technical challenge for genome assembly and alignment programs using NGS data. RFGR is a comprehensive tool that can find exact repetitive sequences in complete genomes and assembled genomes, as well as NGS reads of prokaryotes. For complete genomes, RFGR uses a suffix trees to find seed repeats of repetitive sequences of fixed length with indels. For assembled genomes, RFGR uses a modified Bowtie aligner to find seed repeats of exact repetitive sequences in the contigs/ scaffolds, which are then extended to maximal repeats. The repeats are classified and for repeats near a gene, RFGR reports the gene as well. For the control dataset of E. coli UTI89 and E. coli K12, RFGR reports 35,141 and 49,352 repeats, respectively. For NGS reads, RFGR uses the frequency of the repetitive k-mers to determine FASTQ reads containing repetitive sequences and removes them from the dataset. An E. coli K12 NGS dataset pre-processed using RFGR, on comparison with the original dataset, gives an improved assembly. The N50 value improves by 22.86% with a decrease in size of the assembly graph by nearly 50%. Thus, with RFGR, we achieve a better assembly with reduced computation. RFGR can be improved in terms of the length of the minimum repeat found, extending to find approximate repeats and to be applicable to Eukaryotes as well.

An Effective Virtual Reality Paradigm for Robotic Assembly in First-Year Engineering Curriculum

An effective Augmented Reality and Virtual Reality paradigm is proposed to facilitate introductory robotics course in the first-year engineering curriculum. The AR/VR Application utilization and its impact on the students' learning with respect to robotic assembly and robotic application programming is emphasized in this article. The paper delves into a comprehensive review of the related works presented in the literature. The requirements for the physical assembly and virtual assembly of movable robots are meticulously highlighted. To facilitate course learning a robotic workshop involving steps introduction to robotics, and practical experience on the robot is conducted. The delivery of the course content is made much more effective by inculcating the Virtual experience of the Robotic assembly process. The virtual robotic assembly and manual physical robotic assembly process processes have their own uniqueness and importance and it is left to the students to pick them on a priority basis. Finally, the effectiveness of the proposed course is determined by conducting an online quiz, collecting student feedback, tabulating and analyzing the results.The results demonstrate the effectiveness of the proposed method in creating interest in robotics and related courses among first-year engineering students. Keywords— Augmented Reality(AR), Virtual Reality(VR), Build Your Own Robot(BYOR), Robotic assembly.

Prof. İbrahim Özdemir will talk about Mizan in the New York Youth Assembly program...

Prof. İbrahim Özdemir will talk about Mizan in the New York Youth Assembly program...

Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice.

Nucleotide base composition plays an influential role in the molecular mechanisms involved in gene function, phenotype, and amino acid composition. GC content (proportion of guanine and cytosine in DNA sequences) shows a high level of variation within and among species. Many studies measure GC content in a small number of genes, which may not be representative of genome-wide GC variation. One challenge when assembling extensive genomic data sets for these studies is the significant amount of resources (monetary and computational) associated with data processing, and many bioinformatic tools have not been optimized for resource efficiency. Using a high-performance computing (HPC) cluster, we manipulated resources provided to the targeted gene assembly program, automated target restricted assembly method (aTRAM), to determine an optimum way to run the program to maximize resource use. Using our optimum assembly approach, we assembled and measured GC content of all of the protein-coding genes of a diverse group of parasitic feather lice. Of the 499 426 genes assembled across 57 species, feather lice were GC-poor (mean GC = 42.96%) with a significant amount of variation within and between species (GC range = 19.57%-73.33%). We found a significant correlation between GC content and standard deviation per taxon for overall GC and GC3, which could indicate selection for G and C nucleotides in some species. Phylogenetic signal of GC content was detected in both GC and GC3. This research provides a large-scale investigation of GC content in parasitic lice laying the foundation for understanding the basis of variation in base composition across species.

‘Al-Mizan’ was discussed in the New York Youth Assembly program

‘Al-Mizan’ was discussed in the New York Youth Assembly program

Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time

Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from practical issues (size and errors of real data), and from the fact that problem formulations inherently admit multiple solutions. Given these, at their core, most state-of-the-art assemblers are based on finding non-branching paths ( unitigs ) in an assembly graph. While such paths constitute only partial assemblies, they are likely to be correct. More precisely, if one defines a genome assembly solution as a closed arc-covering walk of the graph, then unitigs appear in all solutions, being thus safe partial solutions. Until recently, it was open what are all the safe walks of an assembly graph. Tomescu and Medvedev (RECOMB 2016) characterized all such safe walks ( omnitigs ), thus giving the first safe and complete genome assembly algorithm. Even though maximal omnitig finding was later improved to quadratic time by Cairo et al. (ACM Trans. Algorithms 2019), it remained open whether the crucial linear-time feature of finding unitigs can be attained with omnitigs. We answer this question affirmatively, by describing a surprising O(m) -time algorithm to identify all maximal omnitigs of a graph with n nodes and m arcs, notwithstanding the existence of families of graphs with Θ (mn) total maximal omnitig size. This is based on the discovery of a family of walks ( macrotigs ) with the property that all the non-trivial omnitigs are univocal extensions of subwalks of a macrotig. This has two consequences: (1) A linear-time output-sensitive algorithm enumerating all maximal omnitigs. (2) A compact O(m) representation of all maximal omnitigs, which allows, e.g., for O(m) -time computation of various statistics on them. Our results close a long-standing theoretical question inspired by practical genome assemblers, originating with the use of unitigs in 1995. We envision our results to be at the core of a reverse transfer from theory to practical and complete genome assembly programs, as has been the case for other key Bioinformatics problems.

ISOLATION OF A NOVEL ANTIMICROBIAL POLYPEPTIDE FROM AN Aspergillus niger ISOLATE

In this study the extracellular proteins from the isolate LC3 belonging to Aspergillus were purified for new antimicrobial polypeptide (AMP) discovery and then tested for antimicrobial activity against Staphylococcus aureus (ATCC 25923) and Methicillin-resistant S. aureus (MRSA). Antimicrobial activity was determined by the trypsin/proteinase K assay, which was polypeptide-based, and it was observed that this protein was a protein of about 11 kDa by gel overlay assay. The minimum inhibitory concentration of purified AMP molecule against S. aureus ATCC 25923 and MRSA was 8 µg/ml and 32 µg/ml, respectively and the AMP molecule was confirmed. ITS sequence analysis showed that isolate LC3 was identified as Aspergillus niger, using the Bioedit sequence assembly program. The sequence was deposited with the GenBank database with accession number MK332597. The results indicate that the purified AMP molecule has the potential to be used in infections caused by S. aureus.

A Global Correction Framework for Camera Registration in Video See-Through Augmented Reality Systems

Abstract Augmented reality (AR) enhances the user’s perception of the real environment by superimposing virtual images generated by computers. These virtual images provide additional visual information that complements the real-world view. AR systems are rapidly gaining popularity in various manufacturing fields such as training, maintenance, assembly, and robot programming. In some AR applications, it is crucial for the invisible virtual environment to be precisely aligned with the physical environment to ensure that human users can accurately perceive the virtual augmentation in conjunction with their real surroundings. The process of achieving this accurate alignment is known as calibration. During some robotics applications using AR, we observed instances of misalignment in the visual representation within the designated workspace. This misalignment can potentially impact the accuracy of the robot’s operations during the task. Based on the previous research on AR-assisted robot programming systems, this work investigates the sources of misalignment errors and presents a simple and efficient calibration procedure to reduce the misalignment accuracy in general video see-through AR systems. To accurately superimpose virtual information onto the real environment, it is necessary to identify the sources and propagation of errors. In this work, we outline the linear transformation and projection of each point from the virtual world space to the virtual screen coordinates. An offline calibration method is introduced to determine the offset matrix from the head-mounted display (HMD) to the camera, and experiments are conducted to validate the improvement achieved through the calibration process.

Performance of qualitative characters of head and grain of local gogo rice from Padang Lawas

The performance of plant qualitative characters is a very important early stage in plant breeding programs that are influenced by simple genes. This is the basis for selecting parent sources in the assembly program for new high-yielding varieties. This research was conducted in August 2022 without a design (plant per row). The results showed that there were 6 individuals with green stems and 1 individual with yellowish green color. Based on the color character of the base of the stem, 5 individuals were found to be green, 1 individual was green with purple stripes and 1 individual was purple. In the leaf color character, there were 3 green individuals, 3 dark green individuals and 1 light green individual. There are 5 white individuals and 2 red individuals based on the character of the color of the rice. If based on the character of grain color there are 6 individuals with yellow color and 1 individual with brownish yellow color and if based on the character of the presence of grain tails there are 6 individuals who do not have grain tails and 1 individual has grain tails.

Comparison of assembly platforms for the assembly of the nuclear genome of Trichoderma harzianum strain PAR3

BackgroundTrichoderma is a diverse genus of fungi that includes several species that possess biotechnological and agricultural applications, including the biocontrol of pathogenic fungi and nematodes. The mitochondrial genome of a putative strain of Trichoderma harzianum called PAR3 was analyzed after isolation from the roots of Scarlet Royal grapevine scion grafted to Freedom rootstock, located in a grapevine vineyard in Parlier, CA, USA. Here, we report the sequencing, comparative assembly, and annotation of the nuclear genome of PAR3 and confirm its identification as a strain of T. harzianum. We subsequently compared the genes found in T. harzianum PAR3 to other known T. harzianum strains. Assembly of Illumina and/or Oxford Nanopore reads by the popular long-read assemblers, Flye and Canu, and the hybrid assemblers, SPAdes and MaSuRCA, was performed and the quality of the resulting assemblies were compared to ascertain which assembler generated the highest quality draft genome assembly.ResultsMaSuRCA produced the most complete and high-fidelity assembly yielding a nuclear genome of 40.7 Mb comprised of 112 scaffolds. Subsequent annotation of this assembly produced 12,074 gene models and 210 tRNAs. This included 221 genes that did not have equivalent genes in other T. harzainum strains. Phylogenetic analysis of ITS, rpb2, and tef1a sequences from PAR3 and established Trichoderma spp. showed that all three sequences from PAR3 possessed more than 99% identity to those of Trichoderma harzianum, confirming that PAR3 is an isolate of Trichoderma harzianum. We also found that comparison of gene models between T. harzianum PAR3 and other T. harzianum strains resulted in the identification of significant differences in gene type and number, with 221 unique genes identified in the PAR3 strain.ConclusionsThis study gives insight into the efficacy of several popular assembly platforms for assembly of fungal nuclear genomes, and found that the hybrid assembler, MaSuRCA, was the most effective program for genome assembly. The annotated draft nuclear genome and the identification of genes not found in other T. harzainum strains could be used to investigate the potential applications of T. harzianum PAR3 for biocontrol of grapevine fungal canker pathogens and as source of anti-microbial compounds.

Seeing double on Cannabis: Haploids and heteroploids of Bipolaris gigantea on hemp and other dicots

ABSTRACT Bipolaris gigantea (= Drechslera gigantea) causes Bipolaris leaf spot (BLS), a devastating and widespread disease on industrial hemp (Cannabis sativa). An investigation of relationships of isolates from hemp and other plants indicated variation in ploidy that has not previously been reported for Bipolaris. Isolates were obtained from BLS lesions on hemp and nearby weeds in 11 Kentucky counties and were similar to each other in morphology and growth characteristics. In total, 23 isolates were analyzed by multilocus phylogenetics, of which seven were also chosen for whole genome shotgun sequencing. Genes for RNA polymerase II subunit 2 (RPB2), translation elongation factor 1-α (TEF1), and mating type (MAT1) indicated that 13 of the isolates were haploid with only a single allele each of RPB2 and TEF1 and either the MAT1-1 or MAT1-2 idiomorph, whereas 10 were apparently “heteroploid” with two alleles each of RPB2 and TEF1 and both MAT1 idiomorphs. Haploids all had identical RPB2 alleles except for a 1-bp difference in two isolates, identical TEF1 alleles, and (if present) identical MAT1-2 alleles. Those alleles were also present in each heteroploid along with either of two related but distinct alleles for each gene. In contrast, haploids and heteroploids shared allelic variation of MAT1-1. In total, four haploid and two heteroploid genotypes were identified. Genome sequence data assembled to 30–32 Mb for each of four haploid isolates, but 10–31 Mb larger sizes for each of three heteroploids depending on sequencing platform and assembly program. The haploids and heteroploids caused similar disease on hemp.

PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.

Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.