Local Alignment Research Articles

Molecular characterization of selected endophytic fungi isolate IDGG 3 leaf galing galing (cayratia trifolia L.) with the polymerase chain reaction method

Background: Endophytic fungi live in plant tissues and are usually not harmful to their host plants. One of the host plants for endophytic fungi is bush grape leaves (Cayratia trifolia L.). Objective: The research aimed to determine the molecular characteristics of the endophytic fungi isolates selected IDGG 3 of bush grape leaves. Methods: The test used the polymerase chain reaction method to determine the species-level characteristics using internal transcribed spacers (ITS) 1 and 4. The DNA band was successfully amplified with 500 base pairs with 3000 markers. Results: The fungi isolates selected IDGG 3 of bush grape leaves in molecular identification based on the Basic Local Alignment Search Tool (BLAST) analysis on Genebank NCBI that the IDGG 3 samples of bush grape leaves had a similarity level of 99%, namely Fusarium incarnatum JL5-2, Fusarium incarnatum JL3-4- 1, Fusarium incarnatum CBB-2, Fusarium incarnatum JL3-3, Fusarium incarnatum CBA-3, Fusarium incarnatum CBB-1, Fusarium incarnatum CBA-2, Fusarium chlamydospore, Fusarium cf. Incarnatum, and Fusarium sp. Conclusion: The results of the molecular characteristics of the selected endophytic fungi isolate IDGG 3 galing-galing leaves (Cayratia trifoliata L.) have the closest degree of kinship with the species Fusarium incarnatum JL3-4-1. The importance of the PCR method in the molecular characterization of endophytic fungi, as well as opening opportunities for further exploration of the biotechnological potential of endophytic fungi from Cayratia trifolia L.

Seam estimation based on dense matching for parallax-tolerant image stitching

Image stitching with large parallax poses a significant challenge in the field of computer vision. Existing seam-based approaches attempt to address parallax artifacts by stitching images along seams. However, issues such as object mismatches, disappearances, and duplications still arise occasionally, primarily due to inaccurate alignment of dense pixels or inappropriate seam estimation methods. In this paper, we propose a robust seam-based parallax-tolerant image stitching method that leverages dense flow estimation from state-of-the-art approaches. Firstly, we develop a seam estimation method that does not require pre-estimation of image warping model. Instead, it directly estimates the seam by measuring the local smoothness of the optical flow field and incorporating a penalty term for duplications. Subsequently, we design an iterative algorithm that utilizes the location of estimated seam to solve a spatial smooth warping model and eliminate outlier corresponding pairs. By employing this approach, we effectively address the intertwined challenges of estimating the warping model and seam. Experiment on real-world images shows that our proposed method achieves superior local alignment accuracy near the stitching seam and outperforms other state-of-the-art techniques on visual stitching result. Code is available at https://github.com/zhihao0512/dense-matching-image-stitching.

Clinical Implications of Surgical Resection without Spinal Fixation in Lumbar Dumbbell Tumors: Evaluating Postoperative Lumbar Alignment and Patient Outcomes

This study examined radiographic changes in local and global spinal alignments and clinical outcomes following tumor resection without spinal fixation in patients with lumbar dumbbell tumors (LDTs). We included 28 patients with LDTs who were followed for at least 2 years after surgery. We analyzed variations in the outcome variables by measuring individual coronal and sagittal parameters from radiographs. Clinical outcomes were assessed using the modified McCormick scale, the Japanese Orthopedic Association score, and the visual analog scale. To evaluate the impact of tumor location on these outcomes, we categorized the patients into 3 groups based on tumor location: upper (T12-L1), middle (L2-3), or lower (L4-S1) group. The local and global spinal parameters (including Cobb angle, cervical lordosis, T1 slope, thoracic kyphosis, thoracolumbar kyphosis, lumbar lordosis [global, upper, middle, lower], sacral slope, pelvic incidence, and pelvic tilt) did not show significant changes after surgery. Preoperatively, all patients experienced gait disturbances, but at the final follow-up, nearly all of them (27 cases, 96.4%) could walk without support. The Japanese Orthopedic Association score and visual analog scale demonstrated significant postoperative improvements. There were no statistically significant group differences in postoperative coronal and sagittal profiles or clinical outcomes among the upper, middle, and lower groups. Tumor resection without spinal fixation had no substantial impact on local and global spinal alignments and led to satisfactory clinical outcomes, suggesting that spinal fixation may not always be necessary when resecting LDTs.

CUDASW++4.0: ultra-fast GPU-based Smith–Waterman protein sequence database search

BackgroundThe maximal sensitivity for local pairwise alignment makes the Smith-Waterman algorithm a popular choice for protein sequence database search. However, its quadratic time complexity makes it compute-intensive. Unfortunately, current state-of-the-art software tools are not able to leverage the massively parallel processing capabilities of modern GPUs with close-to-peak performance. This motivates the need for more efficient implementations.ResultsCUDASW++4.0 is a fast software tool for scanning protein sequence databases with the Smith-Waterman algorithm on CUDA-enabled GPUs. Our approach achieves high efficiency for dynamic programming-based alignment computation by minimizing memory accesses and instructions. We provide both efficient matrix tiling, and sequence database partitioning schemes, and exploit next generation floating point arithmetic and novel DPX instructions. This leads to close-to-peak performance on modern GPU generations (Ampere, Ada, Hopper) with throughput rates of up to 1.94 TCUPS, 5.01 TCUPS, 5.71 TCUPS on an A100, L40S, and H100, respectively. Evaluation on the Swiss-Prot, UniRef50, and TrEMBL databases shows that CUDASW++4.0 gains over an order-of-magnitude performance improvements over previous GPU-based approaches (CUDASW++3.0, ADEPT, SW#DB). In addition, our algorithm demonstrates significant speedups over top-performing CPU-based tools (BLASTP, SWIPE, SWIMM2.0), can exploit multi-GPU nodes with linear scaling, and features an impressive energy efficiency of up to 15.7 GCUPS/Watt.ConclusionCUDASW++4.0 changes the standing of GPUs in protein sequence database search with Smith-Waterman alignment by providing close-to-peak performance on modern GPUs. It is freely available at https://github.com/asbschmidt/CUDASW4.

Imaging with a twist: Three-dimensional insights of the chiral nematic phase of cellulose nanocrystals via SHG microscopy.

Cellulose nanocrystals (CNCs) are bio-based nanoparticles that, under the right conditions, self-align into chiral nematic liquid crystals with a helical pitch. In this work, we exploit the inherent confocal effect of second-harmonic generation (SHG) microscopy to acquire highly resolved three-dimensional (3D) images of the chiral nematic phase of CNCs in a label-free manner. An in-depth analysis revealed a direct link between the observed variations in SHG intensity and the pitch. The highly contrasted 3D images provided unprecedented detail into liquid crystal's native structure. Local alignment, morphology, as well as the presence of defects are readily revealed, and a provisional framework relating the SHG response to the orientational distribution of CNC nanorods within the liquid crystal structure is presented. This paper illustrates the numerous benefits of using SHG microscopy for visualizing CNC chiral nematic systems directly in the suspension-liquid phase and paves the road for using SHG microscopy to characterize other types of aligned CNC structures, in wet and dry states.

Identification of new circulating recombinant form of HIV-1 CRF139_02B in Japan, and search for the origin.

Many circulating recombinant forms (CRFs) of HIV-1 have been reported, resulting in complex molecular epidemiology of HIV-1 infection. In this study, we newly identified CRF139_02B in Japan from 4 cases of anti-retroviral therapy naïve people living with HIV. Near full-length genome sequences of CRF139_02B were determined using Illumina MiSeq. Basic Local Alignment Search Tool (BLAST) revealed that there were several sequences having the same breakpoints as CRF139_02B in the UK and Nepal, though its full-length genome sequences were not available. Maximum clade credibility tree analysis using the region of protease and reverse transcriptase of HIV- 1 estimated that the time to the most recent common ancestor of CRF139_02B variants found in Japan was 2017.6 (95% highest posterior density interval: 2015.9-2019.3), and that among the UK, Nepal, and Japan was 2010.4 (2007.8- 2012.5). These results suggested that CRF139_02B circulated in Japan recently and domestically. Furthermore, the origin of CRF139_02B could be in the UK. Because there is a possibility that further international circulation of CRF139_02B may be observed in the near future, continuous monitoring of HIV-1 molecular epidemiology will be needed.

Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods

Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein–protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.Graphical

Risk Factors for Adjacent Vertebral Fractures Following Cement Vertebroplasty: The Clinical Significance of Multiple Preexisting Vertebral Compression Fractures.

A retrospective cohort study. The study retrospectively analyzed the factors associated with the development of adjacent vertebral fractures. Adjacent vertebral fractures (AVF) may occur following cement vertebroplasty, and several risk factors have been reported with controversies. A total of 123 patients, with a mean age of 79.2 years, who underwent single-level vertebroplasty were included in the investigation. We systematically collected data encompassing baseline demographics, osteoporosis parameters, surgical details, radiologic measurements, and Hounsfield unit (HU) values in the lumbar spine. Subsequently, univariable, followed by multivariable logistic regression analyses, were employed to identify the risk factors of AVFs. Thirty of 123 patients had AVFs within 6 months following vertebroplasty. The AVF group exhibited a higher percentage of multiple preexisting vertebral compression fractures (P=0.006), a greater volume of injected cement (P=0.032), and a more pronounced reduction in local kyphosis (P=0.007). Multivariable logistic regression analysis revealed multiple preexisting vertebral compression fractures and a reduction in local kyphosis exceeding 8 degrees were independent risk factors for AVFs (P=0.008 and 0.003, respectively), with odds ratios of 3.78 (95% confidence interval: 1.41-10.12) and 4.16 (95% CI: 1.65-10.50), respectively. Subgroup analysis showed that patients with multiple preexisting vertebral compression fractures (VCFs) had significantly lower bone mineral density Z-score, T-score, and HU values compared with those without preexisting VCFs (P<0.05). Conversely, there were no significant differences in T-score or HU values between patients with no VCFs and those with a single VCF. This study demonstrated that both bone strength and local alignment are key factors associated with adjacent vertebral fractures. Specifically, having multiple preexisting vertebral compression fractures and a reduction in local kyphosis exceeding 8 degrees are independent risk factors. The presence of more than one previous vertebral compression fracture serves as a significant clinical indicator of advanced bone density reduction in patients with osteoporosis, offering a quick and straightforward method for identifying high-risk patients. Patients exhibiting these risk factors should be monitored more closely for favorable clinical outcomes. Level III-retrospective nonexperimental study.

GLTScene: Global‐to‐Local Transformers for Indoor Scene Synthesis with General Room Boundaries

AbstractWe present GLTScene, a novel data‐driven method for high‐quality furniture layout synthesis with general room boundaries as conditions. This task is challenging since the existing indoor scene datasets do not cover the variety of general room boundaries. We incorporate the interior design principles with learning techniques and adopt a global‐to‐local strategy for this task. Globally, we learn the placement of furniture objects from the datasets without considering their alignment. Locally, we learn the alignment of furniture objects relative to their nearest walls, according to the alignment principle in interior design. The global placement and local alignment of furniture objects are achieved by two transformers respectively. We compare our method with several baselines in the task of furniture layout synthesis with general room boundaries as conditions. Our method outperforms these baselines both quantitatively and qualitatively. We also demonstrate that our method can achieve other conditional layout synthesis tasks, including object‐level conditional generation and attribute‐level conditional generation. The code is publicly available at https://github.com/WWalter-Lee/GLTScene.

Facile Electrical DNA Genosensor for Human Papillomavirus (HPV 58) for Early Detection of Cervical Cancer

For decades, a Pap smear test has been applied as a conventional method in detecting Human Papillomavirus caused cervical cancer. False-positive results were also recorded while using it as conventional method. Current biosensor such as Hybrid (II) Capture resulted in higher time consumption and cost. s Meanwhile, in this study we provided facile, mini, rapid, highly sensitive, eco-friendly, and cost-effective sensing system focusing on HPV strain 58 (HPV58) in a nano-size lab-on-chip technology genosensor. 30-mer of virus ssDNA designed and analyzed as a probe via bioinformatics tools such as GenBank, Basic Local Alignment Searching Tools (BLAST) and ClustalW. Nanotechnology-developed colloidal Gold-nanoparticles (AuNPs) are used in the biosensor fabrication to produce high stability and electron efficient transmission during electrical measurement. AuNPs-APTES modified on active sites of IDEs, followed by immobilization of specific probe ssDNA for HPV 58. Hydrogen binding during hybridization with its target produce electrical signals measured by KEITHLEY 2450 (Source Meter). The genosensor validated with different types of targets such as complimentary, non-complementary and single mismatch oligonucleotides. The serial dilution of target concentration has been experimented triplicate (n=3) range from 1fM to 10μM. The slope of calibration curve resulted 2.389E-0 AM-1 with regression coefficient (R2) = 0.97535.

Collective behavior of active filaments with homogeneous and heterogeneous stiffness.

The collective dynamics of active biopolymers is crucial for many processes in life, such as cellular motility, intracellular transport, and division. Recent experiments revealed fascinating self-organized patterns of diverse active filaments, while an explicit parameter control strategy remains an open problem. Moreover, theoretical studies so far mostly dealt with active chains with uniform stiffness, which are inadequate in describing the more complicated class of polymers with varying stiffness along the backbone. Here, using Langevin dynamics simulations, we investigate the collective behavior of active chains with homogeneous and heterogeneous stiffness in a comparative manner. We map a detailed non-equilibrium phase diagram in activity and stiffness parameter space. A wide range of phase states, including melt, cluster, spiral, polar, and vortex, are demonstrated. The appropriate parameter combination for large-scale polar and vortex formation is identified. In addition, we find that stiffness heterogeneity can substantially modulate the phase behaviors of the system. It has an evident destructive effect on the long-ranged polar structure but benefits the stability of the vortex pattern. Intriguingly, we unravel a novel polar-vortex transition in both homogeneous and heterogeneous systems, which is closely related to the local alignment mechanism. Overall, we achieve new insights into how the interplay among activity, stiffness, and heterogeneity affects the collective dynamics of active filament systems.

SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis.

Sesame (Sesamum indicum L., 2n = 26) is a crucial oilseed crop cultivated worldwide. The ancient evolutionary position of the Sesamum genus highlights its value for genomics and molecular genetics research among the angiosperms of other genera. However, Sesamum is considered a small orphan genus with only a few genomic databases for cultivated sesame to date. The urgent need to construct comprehensive, curated genome databases that include genus-specific gene resources for both cultivated and wild Sesamum species is being recognized. In response, we developed Sesamum Genomics Database (SesamumGDB), a user-friendly genomic database that integrates extensive genomic resources from two cultivated sesame varieties (S. indicum) and seven wild Sesamum species, covering all three chromosome groups (2n = 26, 32, and 64). This database showcases a total of 352 471 genes, including 6026 related to lipid metabolism and 17 625 transcription factors within Sesamum. Equipped with an array of bioinformatics tools such as BLAST (basic local alignment search tool) and JBrowse (the Javascript browser), SesamumGDB facilitates data downloading, screening, visualization, and analysis. As the first centralized Sesamum genome database, SesamumGDB offers extensive insights into the genomics and genetics of sesame, potentially enhancing the molecular breeding of sesame and other oilseed crops in the future. Database URL: http://www.sgbdb.com/sgdb/.

GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses

Grass species, which include the major cereal crops maize, wheat, rice, and sugarcane, are an integral part of our global agriculture and source of food and energy for a growing world population. GRASSIUS was established as a knowledgebase for transcription factors (TFs) and coregulators (CoRegs) in maize and several other species in the grass family. TFs are a primary component of the gene regulatory networks (GRNs) and the underlying gene regulatory grids (GRGs) that govern all aspects of plant growth and metabolism. GRASSIUS is the source for all information pertaining to the maize TFome collection, which serves as a powerful resource for the discovery of GRNs in maize and other cereals [1,2]. Here we describe the release of the GRASSIUS 2.0 knowledgebase (www.grassius.org) with updated data, query, and tool features, as well as the ability to expand to accommodate future datasets. The membership and annotation of all TF and CoReg families has been updated and revised to include gene models from v3, v4, and v5, of the maize B73 genome and recent genome versions of rice, sorghum, Brachypodium, and sugarcane. A translation tool enables cross referencing of Gene IDs between versions of the maize genome. Protein-DNA interactions (PDIs) have been added incorporating results derived from various gene- and TF-centered PDI discovery tools and visualized through a new web-based interface. A filtering tools permits the selection and visualization of PDIs within a ± 2 kb distance from the transcriptional start site (TSS) of a gene of interest. A new BLAST (Basic Local Alignment Search Tool) tool facilitates searching of the maize TFome as well as v3, v4, and v5 TF gene model sets. Lastly, we describe the methodology used to implement GRASSIUS 2.0 which can guide others in developing and updating similar plant gene regulatory knowledgebases.

Genome-wide association study of salt tolerance at the seed germination stage in lettuce.

Developing lettuce varieties with salt tolerance at the seed germination stage is essential since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity-affected growing regions. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate breeding of improved lettuce varieties with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) in lettuce to identify marker-trait association for salt tolerance at the seed germination stage. The study involved 445 diverse lettuce accessions and 56,820 single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology using lettuce reference genome version v8. GWAS using two single-locus and three multi-locus models for germination rate (GR) under salinity stress, 5 days post seeding (GR5d_S) and a salinity susceptibility index (SSI) based on GR under salinity stress and control conditions, 5 days post seeding (SSI_GR5d) revealed 10 significant SNPs on lettuce chromosomes 2, 4, and 7. The 10 SNPs were associated with five novel QTLs for salt tolerance in lettuce, explaining phenotyping variations of 5.85%, 4.38%, 4.26%, 3.77%, and 1.80%, indicating the quantitative nature of these two salt tolerance-related traits. Using the basic local alignment search tool (BLAST) within 100 Kb upstream and downstream of each of the 10 SNPs, we identified 25 salt tolerance-related putative candidate genes including four genes encoding for major transcription factors. The 10 significant salt tolerance-related SNPs and the 25 candidate genes identified in the current study will be a valuable resource for molecular marker development and marker-assisted selection for breeding lettuce varieties with improved salt tolerance at the seed germination stage.

Tip-induced local Fermi level alignment: A Stark shift in vacuum level in scanning tunneling microscope configurations

Electric fields in the junction of a scanning tunneling microscope (STM) are generally considered to have a negligible impact on the vacuum level (VL) of materials. We employed field emission resonance (FER) in the STM, combined with the triangular potential model, to measure the VL of the Ag(100) surface under varying electric currents. Unexpectedly, our results reveal that the VL exhibits a linear positive energy shift with increasing electric field strength. We suggest that this Stark shift in the VL arises from local Fermi level alignment induced by the STM tip. Additionally, we examined the VL of Ag islands grown on Cu(111) and Au(111) surfaces under different currents. Despite the Ag island having a lower work function than the Cu(111) and Au(111) surfaces, the energy shift in the VL with respect to the electric field on the Ag island is almost identical to that on the substrate under the same tip structure. This suggests that the Stark shift of the VL is insensitive to the work function. These findings are crucial for utilizing FER to measure local work function variations on surfaces, as the measured value is not influenced by the STM tip structure or the tunneling current, both of which can alter the electric field.

Robust Edge Flows in Swarming Bacterial Colonies

Understanding if and how the chirality of biomolecules is transferred across scales into larger components and active processes remains elusive. For instance, flagellated bacteria swim in helical trajectories but chirality seems absent from the active turbulence dynamics they display in dense suspensions. We address this question by examining multiscale dynamics in colonies. We find active turbulence without manifest chirality in the bulk, but wide, clockwise (viewed from the air side) circulation all along the tortuous centimeter-scale external boundary, while similar but counterclockwise flows follow internal boundaries. We trace the origin of these robust edge flows to an unexpected asymmetry at the individual level that is amplified by local interactions. We rationalize our findings with a model of noisy self-propelled particles immersed in a Stokes fluid that accounts faithfully for our observations. Our modeling and experimental efforts reveal that local nematic alignment and hydrodynamic interactions amplify the weak chiral bias in individual motion, promoting the formation of strong edge flows. The likely topological protection of these flows provides robust transport mechanism over large scales. Such robust boundary phenomena in weakly chiral active fluids may inspire new control strategies for active and biological matter. Published by the American Physical Society 2024

AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function.

The rapid expansion of biological sequence databases due to high-throughput genomic and proteomic sequencing methods has left a considerable number of identified protein sequences with unclear or incomplete functional annotations. Domains of unknown function (DUFs) are protein domains that lack functional annotations but are present in numerous proteins. To address the challenge of finding functional annotations for DUFs, we have developed a computational method that efficiently identifies and annotates these enigmatic protein domains by utilizing the position-specific iterative basic local alignment search tool (PSI-BLAST) and data mining techniques. Our pipeline identifies putative potential functionalities of DUFs, thereby decreasing the gap between known sequences and functions. The tool can also take user input sequences to annotate. We executed our pipeline on 5111 unique DUF sequences obtained from Pfam, resulting in putative annotations for 2007 of these. These annotations were subsequently incorporated into a comprehensive database and interfaced with a web-based server named "AnnoDUF". AnnoDUF is freely accessible to both academic and industrial users, via the World Wide Web at the link http://bts.ibab.ac.in/annoduf.php. All scripts used in this study are uploaded to the GitHub repository, and these can be accessed from https://github.com/BioToolSuite/AnnoDUF.

Accelerating DNA Sequence Alignment using Altera DE2-115

DNA sequence alignment is a technique for discovering information between two base sequences which the Smith-Waterman algorithm is the accurate method that provides a precise result for alignment compared to others. However, the performance was influence by size of dataset and a long DNA base sequence which resulted the time required for the alignment process is much longer in relation to the number of DNA sequence samples. There are many ways to accelerate DNA sequence alignment, and Field Programmable Gate Array (FPGA) is a good choice due to its parallel processing and cost efficiency. Although FPGA acceleration approaches are not new, this work investigates a purely software-based FPGA acceleration using the Altera Cyclone IV EP4CE115F29C7N FPGA as the target device. The SW algorithm was developed using the C language in Quartus II version 18.1 and the Nios II software build tools for Eclipse. The development starts with setting up the Qsys architecture before developing the code in Eclipse to determine the computational performance. The result shows the computational timing and speed of the implementation, with the highest speed achieved being 198.76 cells per millisecond. To summarise, the computational performance ultimately depends on the maximum matrix size of the FPGA, which is also influenced by the DNA-based pair length and able to complete using low-cost FPGA.

The expanding role of cap-adjacent modifications in animals

Eukaryotic mRNA cap structures directly influence mRNA stability, translation, and immune recognition. While the significance of the mRNA cap itself has been well-established, recent research has revealed the intricate modifications to the nucleotides immediately adjacent to the cap. These include 2′-O-methylation (Cap1, Cap2) and N6-methyladenosine (m6Am), which recent work suggests may be dynamically regulated, interdependent, and vital for gene-regulation. This perspective explores the expanding role of cap-adjacent modifications. Cap1 is found on metazoan mRNA, viruses which infect metazoans, and the COVID-19 mRNA vaccines. We combined basic local alignment and 2D-TLC to track cap-adjacent modifying proteins and the modifications themselves to profile their prevalence throughout eukaryotes. We confirm that Cap1 is broadly metazoan specific, but surprisingly also in a brown algae. Additionally, we find genomic presence of the eraser, FTO more predictive of the occurrence of m6Am than the m6Am-writer, PCIF1. We then outline future directions to understand and exploit these enigmatic modifications.

Legal Hermeneutics: A Standard and Parameters of Interpretation of the New Criminal Code

The purpose of this study is to investigate how standards and parameter for interpreting the Kitab Undang-Undang Hukum Pidana (KUHP) were developed. Public believes that the KUHP contains a number of contentious sections. This study is a type of qualitative research through library data. It is called library research because data regarding legal interpretation and the formation of standards and parameters are obtained from library materials. The text analysis method with a multidisciplinary, interdisciplinary, and transdisciplinary approach to science will be employed as the data analysis technique. In this study, authoritative and original data serve as the primary source, while supporting data from multiple sources serves as the secondary source. scholarly writings, news articles or official reports, commentary on the recently. This research finds that hermeneutics as legal interpretation serves as a bridge between law and moral ethics. There are 6 standards and parameters in the process of legal interpretation, namely text and legal context analysis, contextual interpretation, methodological interpretation, dialogue between the text and the interpreter, principles of justice and humanity, evaluation, and validity testing. Finally, the results of applying those standards and parameters in examining Pasal 2 ayat (2) KUHP regarding common law emphasize the importance of balancing respect for local wisdom and alignment with national legal principles.