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Mashup Score: 0CRISPR/Cas-based genome editing for cyanophage of Anabeana sp. - 2 hour(s) ago
Efforts have been directed towards genome editing in cyanobacteria, yet achieving genome reduction in cyanophages remains a challenging task. In this study, we utilized the CRISPR-Cas12a system to successfully delete multiple genes within A-1(L) and A-4(L) cyanophages. Through careful manipulation, we generated a deletion mutant cyanophage with a 2,778 bp reduction in genome size, representing a 6.6% decrease compared to the wild type (WT). In summary, our research has introduced a robust method for gene editing in cyanophages, facilitating the identification of nonessential genes essential for cyanophage propagation. This advancement holds promise in addressing the widespread issue of water blooms and the associated environmental hazards. ### Competing Interest Statement The authors have declared no competing interest.
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Mashup Score: 0Echoes of self: Understanding acoustic structure and informational content in common marmoset (Callithrix jacchus) phee sequences - 2 hour(s) ago
Communication in social animals relies heavily on acoustic cues, yet many species possess limited vocal repertoires. To compensate, animals often produce vocalizations in sequences, potentially enhancing the diversity of transmitted information. However, the significance of repeated elements within these sequences remains poorly understood. Here, we investigated the spectro-temporal structure of elements within common marmoset ( Callithrix jacchus ) phees, a long-distance contact call, often produced in sequences. Employing machine learning techniques (random forests) and linear mixed effects models, we explored how elements varied based on their position within sequences and assessed their ability to encode identity and sex information. Additionally, we examined similarities between elements occupying the same position in different sequences. Our results reveal structural differences both within and between sequences, with variations observed in phees at different positions within the
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Mashup Score: 1A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk - 3 hour(s) ago
Evolution by natural selection is expected to be a slow and gradual process. In particular, the mutations that drive evolution are predicted to be small and modular, incrementally improving a small number of traits. However, adaptive mutations identified early in microbial evolution experiments, cancer, and other systems often provide substantial fitness gains and pleiotropically improve multiple traits at once. We asked whether such pleiotropically adaptive mutations are common throughout adaptation or are instead a rare feature of early steps in evolution that tend to target key signaling pathways. To do so, we conducted barcoded second-step evolution experiments initiated from five first-step mutations identified from a prior yeast evolution experiment. We then isolated hundreds of second-step mutations from these evolution experiments, measured their fitness and performance in several growth phases, and conducted whole-genome sequencing of the second-step clones. Here, we found tha
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Mashup Score: 2Improved Python Package for DNA Sequence Encoding using Frequency Chaos Game Representation - 5 hour(s) ago
Frequency Chaos Game Representation (FCGR), an extended version of Chaos Game Representation (CGR), emerges as a robust strategy for DNA sequence encoding. The core principle of the CGR algorithm involves mapping a one-dimensional sequence representation into a higher-dimensional space, typically in the two-dimensional spatial domain. This paper introduces a use case wherein FCGR serves as a kmer frequency-based encoding method for motif classification using a publicly available dataset. Availability and implementation: The FCGR python package, use case, along with additional functionalities, is available in the GitHub. Our FCGR package demonstrates superior accuracy and computational efficiency compared to a leading R-based FCGR library {lochel2020deep}, which is designed for versatile tasks, including proteins, letters, and amino acids with user-defined resolution. Nevertheless, it is important to note that our Python package is specifically designed for DNA sequence encoding, where
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Mashup Score: 0Fine Mapping and Candidate Gene Analysis of Dravet Syndrome Modifier Loci on Mouse Chromosomes 7 and 8 - 9 hour(s) ago
Dravet syndrome is a developmental and epileptic encephalopathy (DEE) characterized by intractable seizures, comorbidities related to developmental, cognitive, and motor delays, and a high mortality burden due to sudden unexpected death in epilepsy (SUDEP). Most Dravet syndrome cases are attributed to SCN1A haploinsufficiency, with genetic modifiers and environmental factors influencing disease severity. Mouse models with heterozygous deletion of Scn1a recapitulate key features of Dravet syndrome, including seizures and premature mortality; however, severity varies depending on genetic background. Here, we refined two Dravet survival modifier ( Dsm ) loci, Dsm2 on chromosome 7 and Dsm3 on chromosome 8, using interval-specific congenic (ISC) mapping. Dsm2 was complex and encompassed at least two separate loci, while Dsm3 was refined to a single locus. Candidate modifier genes within these refined loci were prioritized based on brain expression, strain-dependent differences, and biologic
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Mashup Score: 0
From early in life, experiences like prenatal stress profoundly affect long-term health and behavior. Maternal stress increases fetal exposure to glucocorticoids (GC), disrupting neurodevelopment and raising susceptibility to psychiatric disorders. Previous studies on synthetic GCs, such as dexamethasone (DEX), revealed impairments in neurogenesis and dendritic spine development. However, the influence of prenatal stress on the gliovascular interface remains unclear. This interface, involving the relationship between astrocytes and blood vessels, is essential for healthy brain development. Our study demonstrates that prenatal stress alters the expression and localization of astrocytic proteins crucial for maintaining vascular homeostasis, such as aquaporin-4, in female offspring exposed to DEX. While overall vascular density remains unaffected, it triggers morphological changes. Particularly, the hippocampus and prefrontal cortex exhibit heightened vulnerability to these effects. This
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Mashup Score: 2Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium - 10 hour(s) ago
Combinations of transcription factors govern the identity of cell types, which is reflected by enhancer codes in cis-regulatory genomic regions. Cell type-specific enhancer codes at nucleotide-level resolution have not yet been characterized for the mammalian neocortex. It is currently unknown whether these codes are conserved in other vertebrate brains, and whether they are informative to resolve homology relationships for species that lack a neocortex such as birds. To compare enhancer codes of cell types from the mammalian neocortex with those from the bird pallium, we generated single-cell multiome and spatially-resolved transcriptomics data of the chicken telencephalon. We then trained deep learning models to characterize cell type-specific enhancer codes for the human, mouse, and chicken telencephalon. We devised three metrics that exploit enhancer codes to compare cell types between species. Based on these metrics, non-neuronal and GABAergic cell types show a high degree of regu
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Mashup Score: 1
The north Black Sea (Pontic) Region was the nexus of the farmers of Old Europe and the foragers and pastoralists of the Eurasian steppe, and the source of waves of migrants that expanded deep into Europe. We report genome-wide data from 78 prehistoric North Pontic individuals to understand the genetic makeup of the people involved in these migrations and discover the reasons for their success. First, we show that native North Pontic foragers had ancestry not only from Balkan and Eastern hunter-gatherers but also from European farmers and, occasionally, Caucasus hunter-gatherers. More dramatic inflows ensued during the Eneolithic, when migrants from the Caucasus-Lower Volga area moved westward, bypassing the local foragers to mix with Trypillian farmers advancing eastward. People of the Usatove archaeological group in the Northwest Pontic were formed ca. 4500 BCE with an equal measure of ancestry from the two expanding groups. A different Caucasus-Lower Volga group, moving westward in a
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Mashup Score: 0Identification of Pappa and Sall3 as Gli3 direct target genes acting downstream of cilia signalling in corticogenesis - 10 hour(s) ago
The cerebral cortex is critical for advanced cognitive functions and relies on a vast network of neurons to carry out its highly intricate neural tasks. Generating cortical neurons in accurate numbers hinges on cell signalling orchestrated by primary cilia to coordinate the proliferation and differentiation of cortical stem cells. While recent research has shed light on multiple ciliary roles in corticogenesis, specific mechanisms downstream of cilia signalling remain largely unexplored. We previously showed that an excess of early-born cortical neurons in mice mutant for the ciliary gene Inpp5e was rescued by re-introducing Gli3 repressor. By comparing expression profiles between Inpp5e and Gli3 mutants, we here identified novel Gli3 target genes. This approach highlighted the transcription factor gene Sall3 and Pappalysin1 (Pappa), a metalloproteinase involved in IGF signalling, as up-regulated genes. Further examination revealed that Gli3 directly binds to Sall3 and Pappa enhancers
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Mashup Score: 0PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing - 13 hour(s) ago
Background: Tracking of Insertions and DEletions (TIDE) analysis, which computationally deconvolves capillary sequencing data derived from the DNA of bulk or clonal cell populations to estimate the efficiency of targeted mutagenesis by programmable nucleases, has played a significant role in the field of genome editing. However, the detection range covered by conventional TIDE analysis is limited. Range extension for deconvolution is required to detect larger deletions and insertions (indels) derived from genome editing in TIDE analysis. However, extending the deconvolution range introduces uncertainty into the deconvolution process. Moreover, the accuracy and sensitivity of TIDE analysis tools for large deletions (>50 bp) remain poorly understood. Results: In this study, we introduced a new software called PtWAVE that can detect a wide range of indel sizes, up to 200 bp. PtWAVE also offers options for variable selection and fitting algorithms to prevent uncertainties in the model. We
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CRISPR/Cas-based genome editing for cyanophage of Anabeana sp. https://t.co/37bk9KZ7Gl #bioRxiv