Transduction of Lentiviral Vectors and ADORA3 in HEK293T Cells Modulated in Gene Expression and Alternative Splicing

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(9), P. 4431 - 4431

Published: May 7, 2025

For steady transgenic expression, lentiviral vector-mediated gene delivery is a commonly used technique. One question that needs to be explored how external vectors and overexpressed genes perturb cellular homeostasis, potentially altering transcriptional networks. In this study, two Human Embryonic Kidney 293T (HEK293T)-derived cell lines were established via transduction, one overexpressing green fluorescent protein (GFP) the other co-overexpressing GFP ADORA3 following puromycin selection ensure stable genomic integration. Genes with differentially transcript utilization (gDTUs) expressed (DEGs) across identified after short-read long-read RNA-seq. Only 31 discovered have changed in expression when was expressed, although hundreds of showed variations use. contrast, even co-overexpression alters more than 1000 genes, there are still less gDTUs. Moreover, DEGs linked overexpression play major role RNA splicing, whereas gDTUs highly number malignancies molecular mechanisms underlie them. analysis data from derived HEK293T, our findings provide important insights into changes alternative splicing.

Language: Английский

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Chromosome-scale assemblies of S. malaccense, S. aqueum, S. jambos, and S. syzygioides provide insights into the evolution of Syzygium genomes

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 6, 2023

Syzygium is a large and diverse tree genus in the Myrtaceae family. Genome assemblies for clove ( aromaticum , 370 Mb) sea apple grande 405 provided first insights into genomic features evolution of genus. Here, we present additional de novo chromosome-scale genome malaccense, aqueum, jambos syzygioides. profiling analyses show that S. malaccense like diploid (2n = 2x 22), while aqueum syzygioides specimens are autotetraploid 4x 44). The (430 Mb), (392 (426 (431 highly complete (BUSCO scores 98%). Comparative genomics showed conserved organization 11 chromosomes with revealed species-specific evolutionary dynamics long terminal repeat retrotransposon elements belonging to Gypsy Copia lineages. This set genomes valuable resource future structural functional comparative studies on species.

Language: Английский

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Improved Genome Sequence of Australian Methicillin-Resistant Staphylococcus aureus Strain JKD6159

Microbiology Resource Announcements, Journal Year: 2023, Volume and Issue: 12(2)

Published: Jan. 18, 2023

Staphylococcus aureus strain JKD6159 represents a prominent community-acquired methicillin-resistant S. (MRSA) clone in Australia. Here, we report an improved assembly of the original genome sequence. By using deep sequencing with multiple technologies combined carefully curated and polishing, believe to contain zero errors.

Language: Английский

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Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 30, 2024

Entomopathogenic fungi belonging to the Order Hypocreales are renowned for their ability infect and kill insect hosts, while endophytic mode of life beneficial rhizosphere effects on plant hosts have only been recently recognized. Understanding molecular mechanisms underlying different lifestyles could optimize potential as both biocontrol biofertilizer agents, well wider appreciation niche plasticity in fungal ecology. This study describes comprehensive whole genome sequencing analysis one most effective entomopathogenic EPF strains, Metarhizium brunneum V275 (commercially known Lalguard Met52), achieved through Nanopore Illumina reads. Comparative genomics exploring intraspecies variability analyses key gene sets were conducted with a second strain, M. ARSEF 4556. The search strain- or species-specific genes was extended strain 3297 other species genus Metarhizium, identify putative adaptations associated differences. Genome size differed significantly, having largest amongst strains sequenced date. revealed an abundance plant-degrading enzymes, colonization-associated genes, intriguing variations regarding predicted secondary metabolic compounds number localization Transposable Elements. significance differences found between closely related fungi, growth-promoting abilities, discussed, enhancing our understanding diverse functionalities applications agriculture

Language: Английский

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Nuclear and Mitochondrial Genome Assemblies of the Beetle, Zygogramma bicolorata, a Globally Important Biocontrol Agent of Invasive Weed Parthenium hysterophorus

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(10)

Published: Oct. 1, 2023

Implementing a genetic-based approach to achieve the full potential of classical biocontrol programs has been advocated for decades. The availability genome-level information brings opportunity scrutinize traits their efficacy and evolvability. However, implementation this advocacy remains limited few instances. Biocontrol globally noxious weed, Parthenium hysterophorus, by leaf-feeding beetle, Zygogramma bicolorata, in place more than four decades now, with varying levels success. As first step providing improvement program, we describe nuclear mitochondrial assemblies Z. bicolorata. We assembled genome from long-read sequence data, error corrected high-throughput short reads checked contaminants duplication produce 936 Mb genome. With 96.5% Benchmarking Universal Single-Copy Orthologs completeness long terminal repeat assembly index 12.91, present reference-quality that appeared be rich at 62.7% genome-wide consists 29,437 protein-coding regions. detected signature insertion fragments 80 positions comprising 13 kb out 17.9 mitochondria sequence. This genome, along its annotations, provides valuable resource gain further insights into bicolorata improving control invasive weed P. hysterophorus.

Language: Английский

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Nicotiana noctiflora Hook. Genome Contains Two Cellular T-DNAs with Functional Genes

Plants, Journal Year: 2023, Volume and Issue: 12(22), P. 3787 - 3787

Published: Nov. 7, 2023

Agrobacterium (Rhizobium)-mediated transformation leads to the formation of crown galls or hairy roots on infected plants. These effects develop due activity T-DNA genes, gathered a big plasmid, acquired from agrobacteria during horizontal gene transfer. However, lot plant species are known contain such sequences, called cellular T-DNAs (cT-DNAs), and maintain normal phenotypes. Some genes remain intact, which conclusion their functional role in In this study, we present comprehensive analysis cT-DNAs Nicotiana noctiflora Hook. genome, including expression opine identification. Deep sequencing genome revealed presence two different cT-DNAs, NnT-DNA1 NnT-DNA2, intact iaaM, iaaH, acs, orf13, orf13a, orf14. According results, all these most active comparison with other organs, is consistent data cT-DNA species. We also used genetic engineering approaches HPTLC HPLC-MS methods investigate product acs (agrocinopine synthase), turned out be similar agrocinopine A. Overall, study expands our knowledge plants brings us closer understanding possible functions. Further research implications could contribute advancements genetics potentially unveil novel traits practical applications agriculture fields.

Language: Английский

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Complete reference genome assemblies and annotations of three Escherichia coli MRE162 clones

Microbiology Resource Announcements, Journal Year: 2023, Volume and Issue: 12(11)

Published: Oct. 9, 2023

ABSTRACT Escherichia coli MRE162 was originally isolated from a toilet pan in 1949 and since been utilized numerous studies. Here, we sequence, assemble, annotate clones held at three laboratories providing reference-level assemblies. We show the uniqueness of to strains open databases make UK clone publically available.

Language: Английский

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Complete genome sequence of Pseudomonas entomophila strain TVIN-A01

Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: 13(2)

Published: Jan. 18, 2024

The complete genome sequence of Pseudomonas entomophila strain TVIN-A01 is reported in this manuscript. It a commonly used laboratory known to infect insects and, hence, often studied host-pathogen interactions. Oxford Nanopore sequencing and Illumina were performed assemble the completely.

Language: Английский

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Ubiquitous genome streamlined Acidobacteriota in freshwater environments

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 15, 2024

Background Acidobacteriota are abundant in soil, peatlands and sediments, but there so far only a few studies on those freshwater environments. Genome streamlined bacteria have reduced genomes as an evolutionary process to adapt oligotrophic environments such oceans lakes. UBA12189, genus under the family Holophagaceae, is uncultivated lineage with ultra-small genome size found aquatic So far, no detailed genomic analyses were done this lineage. Here, we analyzed 66 MAGs of UBA12189 (metagenome assembled genomes; including 2 complete genomes) from lakes rivers Europe, North America Asia, which first reported. Results extremely small sizes (< 1.4Mbp), low GC content highly diverse pangenome. In lakes, bacterial surface waters (epilimnion) down 300 meters depth (hypolimnion). appears be free-living CARD-FISH analysis, concrete evidence host association. Comparative analysis shows that compared other Nanopelagicales Methylopumilus, reduction has caused more limited metabolic repertoire carbon, sulfur nitrogen metabolisms, well higher degree auxotrophy various amino acids, vitamins sulfur. also very numbers membrane transporters. Interestingly, proportion unannotated genes (10% – 14%) pangenome, suggesting unknown trove potential for environmental adaptation. Despite having genomes, encodes proteorhodopsin, cbb₃-type cytochrome c oxidases biosynthesis pathways heme, vitamin K₂ B₂ (riboflavin). These may give selective advantage during streamlining process. We propose new ‘Ca. Acidiparvus’ within two species named ‘A. lacustris’ fluvialis’. Acidiparvus described phylum Acidobacteriota, free-living, slow-growing scavenger Conclusion This study explores ecology genomics yet another bacterium. With repertoires co-occurring microorganisms observed, future cultivated crucial. Metagenomics alone cannot identify non-canonical pathways, especially considering high Acidiparvus.

Language: Английский

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HyDRA: a pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 27, 2024

ABSTRACT Background Short-read RNA sequencing (RNAseq) has widely been used to sequence from a wide range of different tissues, developmental stages and species. However, the technology is limited by inherent biases its inability capture full-length transcripts. Long-read RNAseq overcomes these issues providing reads that can span multiple exons, resolve complex repetitive regions capability cover entire Unfortunately, this still prone higher error rates. Noncoding transcripts are highly specific cell types tissues remain underrepresented in current reference annotations. This problem exacerbated dismissal sequenced align genomic do not contain annotated transcripts, resulting approximately half expressed being overlooked transcriptional studies. Results We have developed pipeline, named HyDRA ( Hy brid d e novo R NA ssembly), which combines precision short with structural resolution long reads, enhancing accuracy reliability custom transcriptome assemblies. Deep, short- long-read data derived ovarian fallopian tube samples were develop, validate assess efficacy HyDRA. identified more than 50,000 high-confidence noncoding RNAs, most previously detected using traditional methods. Conclusions HyDRA’s assembly performed 40% better similar obtained top-ranked stand-alone de short-read-only tool over 30% one best-in-class multistep approach. Although rapidly advancing, vast availability short-read will ensure hybrid approaches like implemented continue be relevant, allowing discovery within tissues. As practice performing assemblies becomes commonplace, advance annotation coding expand our knowledge genome.

Language: Английский

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