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Human cancer cell lines are widely used in artificial culture systems to study cancer biology due to their immortalization, enabling extended culturing compared to primary cells. However, genomic instability can rapidly alter cellular behavior, raising questions about the transcriptome stability for controlled studies. We cultivated HCT-116 cells over 25 passages (~16 weeks), and observed a stable transcriptome up to passage 20, with only minimal differential gene expression. Above passage 20, genes corresponding to cell proliferation and cell death were upregulated suggesting a change in general cellular regulation and underlining defined cell culture time periods for stable and reproducible experimental conditions.
[This corrects the article DOI: 10.17912/micropub.biology.000693.].
[This corrects the article DOI: 10.17912/micropub.biology.002076.].
We identify an endoderm-restricted organelle in published volume electron microscopy datasets of C. elegans embryos. The organelle consists of a tubular ring surrounding a membrane-bound compartment harboring a prominent densely stained particle and exhibits a basal polarity concordant with canonical gut granules. This finding offers ultrastructural detail to recent evidence that gut granules are bi-lobed organelles with two distinct compartments.
DICER1 syndrome is a rare cancer predisposition disorder linked to disruption of the miRNA biogenesis enzyme Dicer. To model germline DICER1 loss, we generated heterozygous knockout cell lines in mouse and human systems. While global miRNA levels were largely unaffected, the let-7 family was consistently downregulated across all models. The coordinated reduction of both guide and passenger strands, without similar effects on co-transcribed miRNAs, indicates a post-transcriptional biogenesis mechanism. These findings reveal a selective sensitivity of let-7 miRNAs to Dicer dosage and suggest a role for let-7 dysregulation in DICER1-associated tumorigenesis.
Communication between the gut and the nervous system coordinates aspects of behavior and responses to stressors. When actively feeding, C. elegans executes a digestive motor program triggered by a calcium wave that requires gap junctional connections along the intestinal length. Loss of function of the innexin-16 ( inx-16 ) gap junctional subunit results in altered group feeding behavior, leading to social feeding characterized by increased body contact, or clumping, between animals. Using genetic analysis, our data shows that inx-16 genetically interacts with npr-1 and flp-21 , but not daf-7 . Thus, gut-to-brain signaling influences social versus solitary feeding behavioral choice.
Developing a gene model for the Glutathione S transferase O3 ortholog ( GstO3 ) in the ASM1815212v1 Genome Assembly (GenBank Accession: GCA_018152125.1) of Drosophila dunni . This ortholog was characterized as part of a developing dataset for a comparative study of detoxification gene family evolution in the immigrans - tripunctata radiation of the genus Drosophila using an adapted Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
Salmonella enterica serovar Typhimurium ( S. Typhimurium) is an intracellular pathogen that employs specialized virulence factors to survive and replicate within host cells, including a putative chitobiose ( chb) operon traditionally associated with chitin utilization. Because chitin is absent in mammalian hosts, its role during infection remains unclear. Here, we investigate the functional potential of the S. Typhimurium chb operon, with particular focus on ChbF, annotated as a 6-phospho-β-glucosidase. Together, our findings support a possible model in which the S. Typhimurium chb operon functions as a glycan-processing system that targets host-derived LacNAc-containing glycans and establishes a framework for future functional characterization.
Life is in constant movement, even microscopic bodies like cells. To understand cellular dynamics, or how cells move and interact, we analyse time-lapse microscopy images that highlight cellular structures like membranes and nuclei. The bioimage community has developed automated tracking algorithms to follow cells over time and space, but these tools often require extensive manual parameter tuning and technical expertise. easytrack democratises cell tracking by providing an intuitive graphical interface and automating the parameter optimisation process, making these powerful algorithms accessible to researchers without computational backgrounds.
The field of budding yeast research has long been empowered by the vast array of genetic tools and community resources available. Rescue by mating is one useful tool that entails mating of meiotic spores directly post-germination. This minimal cell division mating process facilitates mating based screens studying the effects of otherwise haploid lethal gene deletions. In this study, we describe the successful application of rescue by mating across two different Saccharomyces species: S. cerevisiae and S. uvarum . This novel inter-species tool enables studies on the evolution of essential genes within the broader Saccharomyces genus.
The evolutionarily conserved RNA-binding protein Muscleblind can function as both a splicing regulator in the nucleus and a mRNA stabilizer in the cytosol. C. elegans mbl-1/ Muscleblind undergoes alternative splicing to generate long and short isoforms that contain one or two KR motifs needed for nuclear localization. We generate three alleles that express MBL-1 proteins with two, one, or no KR motifs and find that the proteins with two KR motifs are restricted in the nucleus and could not promote neurite growth in a sensitized background. Surprisingly, proteins with one or no KR motifs are located in both cytoplasm and nucleus.
Loss of function in the Drosophila melanogaster gene julius seizure ( jus ) causes the fly to have a seizure-like condition known as bang-sensitivity. Here, we characterize the expression patterns of two different jus reporters, a jus -GAL4 construct and a jus protein trap allele, in the central nervous system during the developmental stages that jus expression is required. The majority of cells that expressed the jus -GAL4 construct co-expressed a GAL80 enhancer trap in the homeotic gene teashirt ( tsh ); expression of jus in this subpopulation was necessary to prevent bang-sensitivity.
Aberrant and excess proteins are destroyed by compartment-specific protein quality control mechanisms. In Saccharomyces cerevisiae , endoplasmic reticulum (ER)-associated degradation (ERAD) and inner nuclear membrane (INM)-associated degradation (INMAD) require the Ubc6 and Ubc7 ubiquitin-conjugating enzymes. Ubc6 is an integral membrane protein. By contrast, Ubc7 is a soluble protein tethered to the ER and INM membranes by the transmembrane protein Cue1. Here, we assessed the requirement of Cue1 in resisting proteotoxic stress. CUE1 loss sensitized cells to hygromycin B to a similar extent as UBC7 deletion, consistent with a shared role for Cue1 and Ubc7 in ER and INM protein quality control.
The Eastern Bongo ( Tragelaphus eurycerus isaaci ) is a critically endangered species in the wild. In zoos, animals are common carriers of Extended-Spectrum Beta-Lactamase (ESBL) producing bacteria. The purpose of this study was to determine if the fecal material of an Eastern Bongo from the Great Plains Zoo contained ESBL producing Enterobacteriaceae . Bacteria from this animal were inoculated onto HardyCHROM™ ESBL agar. Isolates with a pink colored colony were subject to whole-genome sequencing. One isolate was identified as Escherichia coli using PubMLST. A putative conjugative plasmid containing seven antimicrobial resistance genes was also found. A Microscan autoSCAN-4 System was then used to determine antimicrobial susceptibility of the isolate. The sequence type identified was (ST/phylogenetic-group/β-lactamase): ST8211/B1/CTX-M-55 + LAP-2 + TEM-1B.
This study examines the specificity and temporal dynamics of Cre drivers in Caenorhabditis elegans somatic gonad development. We use regulatory regions from factors known to be expressed within the Distal Tip Cell (DTC) lineage: hnd-1 p and ceh-22 p drivers exhibit broad expression throughout the somatic gonad; lin-32 p expression is confined to Z1a/Z4p derivatives; and hlh-12 p specifically targets the DTC. Temporal profiling shows hnd-1 p activity from early L1, ceh-22 p from early L2, and lin-32 p and hlh-12 p activity emerging later in L2/L3. Collectively, these results enable the application of Cre-mediated drivers to conditional expression in specific somatic gonad cell types.
Meiosis is a common response to nutrient deprivation in yeasts. Our goal was to determine whether the yeast Saccharomyces paradoxus performed meiosis under other abiotic stress factors, specifically salt stress. We predicted that S. paradoxus meiosis would increase in the presence of salt because osmotic stress activates the IME1 transcription factor in its model yeast relative S. cerevisiae . Contrary to our prediction, the sporulation rate of S. paradoxus decreased as salinity increased. We hypothesize that this is due to salt inhibiting mitochondrial function, but more studies are needed to determine the cause.
Overcoming Lysogenization Defect (OLD) proteins demonstrate anti-phage defense in multi-gene systems including the Gabija system and some retrons, but isolated OLD genes remain poorly understood. Here we show the uncharacterized E. coli gene ybjD encodes an OLD protein producing anti-phage phenotypes upon induced expression. The Toprim domain is dispensable while the ATPase domain is essential for these phenotypes. Unexpectedly, a Walker A mutant predicted to prevent ATP binding retains anti-phage phenotypes but exhibits enhanced cytotoxicity. Together, these findings suggest ATP binding modulates YbjD activity. We propose renaming ybjD as oldB , a Class 1 OLD protein in E. coli .
Tauopathies are neurodegenerative diseases characterized by aggregation of Tau into neurofibrillary tangles. Elucidation of cellular phenomena occurring in degenerative states will be important for long-term mitigation strategies. Here we show two phenotypes involving the synaptic vesicle protein RAB-3 in a Caenorhabditis elegans TauV337M model: a developmental reduction of RAB-3 and an age-related mislocalization in motor axons. We further show that the developmental reduction of RAB-3 is not due to changes in transcriptional expression. We suggest axonal transport and/or synaptic vesicle recycling defects are responsible for developmental and age-related phenotypes.
According to FlyBase, the Drosophila melanogaster (fruit fly) Neprilysin-like 15 (Nepl15) gene has only one annotated transcript and a 686-amino acid-long protein. However, Nepl15 transcripts exhibit organ- and sex-specific differential expression, and Nepl15 knock-out mutation results in sex-dependent contrasting phenotypes. Thus, we investigated whether unreported sex-specific Nepl15 transcripts exist. Our sequencing results of Nepl15 cDNA synthesized from the Oregon-R adult male and female RNA samples show a few changes in the codons, which alter the amino acid sequences in our samples. However, the changes do not impact the subcellular localization or overall Nepl15 protein structure as determined by bioinformatics analyses.
Lineage-based cell identification in C. elegans typically requires intensive live imaging and tracking. Recent methods attempt to automate cell identification on the basis of spatiotemporal atlases. We present EmbAlign, an automated 3D registration framework that determines lineage identities from single embryo snapshots. EmbAlign retrieves reference templates from a spatiotemporal atlas and refines assignments using an iterative Sinkhorn alignment procedure, robustly handling positional variability and arbitrary orientations in uncompressed embryos. EmbAlign achieves 96.9% accuracy up to the 190-cell stage and includes a diagnostic layer for continuous scoring (AUPRC = 0.546), converting raw spatial data into lineage aware datasets.