Aug 2026· Zenodo (CERN European Organization for Nuclear Research)
Abstract
Supplemental data failes to accompany the dissertation titled "The Evolution of Crucial Verterbate Muscle Proteins." Descriptions of files are provided below. Data S1: Myosin expression values and sample metadata from publicly available datasets. The file does not contain Lonchura striata expression data. NCBI accession numbers for both myosin loci and sample expression sets are provided. XLSX format. Data S2: Phylogenetic tree of cardiac myosin sequences with bootstrap support values. Tree is reflected graphically in Supplemental Figure S1. Newick format. Data S3. Multiple sequence alignment of vertebrate cardiac myosins. Alignment was used to generate the tree depicted in Supplemental Figure S1 and included in Data S2. FASTA format. Accession numbers included in sequence IDs. Data S4. List of vertebrate myosin sequences. The file also contains explanations of why sequences may have been excluded or descriptions of any manual edits made. CSV format. Data S5. Phylogenetic tree of avian cardiac myosins with bootstrap support values. This tree is depicted graphically in Figure 4C. Newick format. Data S6. Multiple sequence alignment of avian cardiac myosins. Alignment was used to generate the tree depicted in Figure 4C and included in Data S5. FASTA format. Accession numbers provided in sequence IDs. Data S7. Multiple sequence alignment of passerine and nonpasserine MYH6 and MYH6B sequences. Alignment was used to generate percent identity scores between passerine MYH6, nonpasserine MYH6, and passerine MYH6B. FASTA format. Data S8. Multiple sequence alignment used to generate 100% consensus sites between MYH6 and MYH6B sequences for passerine and nonpasserine birds. FASTA format. Data S9. Multiple sequence alignment of chicken myosin sequences from previous publications and NCBI reference genome. FASTA format. Data S10. Multiple sequence alignment of Sauropsid MYH15. Alignment was used to test for evidence of selection. FASTA format. Data S11. Phylogenetic tree of MYH15 sequences. Tree was used to test for evidence of selection. Newick format. Data S12. Expression data for Lonchura striata hearts. Multi-tabbed spreadsheet with proportion of MYH expressed, summarized MYH expression per sample, and NCBI genes used to quantify MYH expression. XLSX format.
It is concluded that bridging the gap between foundational CRISPR research and its real-world applications is imperative and future efforts should focus on democratizing tools via open-source platforms, advancing delivery systems, and fostering sustainable innovation through synthetic biology integration to fully realize the transformative potential of genome editing in organisms beyond model organisms.
S. Sarsaiya, Archana Jain, Jishuang Chen et al.· Biotechnology Advances· 2 citations
It is argued that formation of a tumour-intrinsic niche is a prerequisite for BRAF-mutant CRC seeding to distant organs and that interference with niche formation may help avoid metastatic relapse.
J. Bugter, L. El Bouazzaoui, E. Küçükköse et al.· bioRxiv· 2 citations
This review summarizes emerging therapeutic strategies for EOC, their mechanisms of action, and their potential to overcome treatment resistance, and covers molecularly targeted therapies, immunotherapies, metabolic and epigenetic approaches, cellular and gene therapies, targeted drug-delivery systems, and locoregional and physical modalities.
Zofia Pietrasik, Mikołaj Kapała, Joanna Pietrasik et al.· Cancers· 0 citations
Genetic engineering (GE) and gene editing may endow traits to trees such as increased biomass and the production of novel biomaterials. Long-lived organisms such as trees might be subject to biotechnology-related risks that could be different than those of annual row crops. Those risks could be relevant to production in engineered plantations and beyond plantations to natural forests. Therefore, appropriate risk regulation is important to assure biosafety of commercialized engineered trees. In addition to gene flow via sexual reproduction, vegetative reproduction might play an additional role in environmental "exposure" risk relative to transgene dispersal in GE tree plantations. While vegetative reproduction is beneficial for preserving desired genetic traits during tree propagation, it may lead to proximal clonal spread in the field. Although the environmental risks associated with vegetative reproduction of GE trees are recognized in commercial forestry, there are few field-based environmental risk assessment (ERA) studies on dispersal risks of self-propagated GE trees. GE or gene editing of target genes involved in the vegetative propagation processes may be useful to mitigate environmental risks of clonal spread through vegetative reproduction. This review provides updates for recent field test results of GE and gene edited trees. Gene candidates related to vegetative reproduction including adventitious shooting (AS) and adventitious rooting (AR) are discussed herein as a means to mitigate unintended clonal spread from GE tree plantations.
The central nervous system (CNS) harbors a distinct immune memory programming system, wherein immunogenic cell death (ICD) acts as a pivotal signaling hub. A spectrum of insults, from systemic metabolic dysfunction to local protein aggregation and ionic dyshomeostasis, can provoke ICD in neurons, glia, and resident immune cells. This process orchestrates the release of damage-associated molecular patterns (DAMPs) from distinct subcellular compartments. These DAMPs synergistically initiate both innate trained immunity (TI), characterized by profound metabolic-epigenetic reprogramming, and antigen-specific adaptive immune responses that traverse the blood-brain barrier. Together, these pathways constitute an integral network of central immune surveillance. Crucially, this ICD-driven immune programming exhibits a striking functional dichotomy depending on the pathological context. In non-neoplastic conditions such as neural injury and neurodegenerative diseases, uncontrolled ICD signaling can establish a pathological trained immune memory, driving a self-perpetuating cycle of chronic neuroinflammation and tissue damage. Conversely, within the tumor microenvironment of malignancies like glioma, the adaptive immune responses elicited by ICD are frequently subverted by potent immunosuppressive mechanisms, culminating in tumor immune escape. This review dissects the differential regulatory mechanisms of ICD-mediated immune memory in CNS tumors versus non-tumor diseases. We aim to elucidate the molecular switches that govern the transition of this immune program from a beneficial, compensatory state to a pathological, detrimental phenotype. By exploring emerging therapeutic strategies, including gene editing, nanomaterials, and bioactive phytochemicals that precisely target ICD pathways, we provide a theoretical framework for understanding CNS immune homeostasis and for the rational design of precision immunotherapies.
Unknown authors· Ageing Research Reviews· 0 citations
Findings establish Cas7-11 as a precise and efficient RNA knockdown tool for functional studies in embryonic development and stem cell biology, providing a versatile alternative to DNA-based gene-editing approaches.
Huan Yan, Imtiaz Ul Hassan, Kai Yan et al.· Cell & Bioscience· 0 citations
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
