Publications by authors named "Ray Enke"

Article Synopsis
  • DNA barcoding uses molecular techniques like DNA extraction, PCR, and Sanger sequencing to identify biological samples.
  • Although it's a valuable tool for hands-on learning in classes, extracting DNA affordably and efficiently from various sample types can be difficult.
  • The text presents two methods that novice students can use to effectively extract DNA from a range of organisms for barcoding purposes.
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Transcriptome analysis through next-generation sequencing (NGS) is an invaluable tool for investigating changes in gene expression across diverse organisms. The nematode () serves as an excellent model organism for dissecting host responses to bacterial infections. Here, our dataset obtained from bulk RNA-sequencing (RNA-seq) can be used to provide in-depth characterization of the mRNA transcriptome profiles of wild-type N2 animals and null mutants of the cytoskeletal regulatory gene /Nav2 following exposure to distinct bacterial environments: their natural laboratory food source, OP50, the human and nematode pathogen PA14, and the emerging pathogen Ag1.

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Retinal degenerative diseases (RDDs) are a diverse group of retinal disorders that cause visual impairment. While RDD prevalence is high, little is known about the molecular mechanisms underlying the pathogenesis within many of these disorders. Here we use transcriptome analysis to elucidate the molecular mechanisms that drive early onset photoreceptor neuron function loss in the mouse model of the RDD Mucolipidosis type IV (MLIV).

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Article Synopsis
  • Retinogenesis is the process where the developing brain transforms into organized retinas, regulated by complex gene networks, but many aspects in humans are still not fully understood.
  • Researchers have used human pluripotent stem cell-derived 3D retinal organoids and Next Generation Sequencing (NGS) to uncover new insights into how cells develop and genes are regulated in the human retina.
  • The study involved creating retinal organoids with specific fluorescent markers and conducting bulk RNA sequencing over a significant developmental period, providing a valuable data set for future vision research.
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Article Synopsis
  • Retinogenesis is the process of forming different types of retinal cells during early development in vertebrates, with challenges in studying human retina due to the need for human fetal tissue.
  • Pluripotent stem cell-derived retinal organoids provide a practical model to investigate these developments, leading to the creation of dual fluorescent reporters to track cellular changes over time.
  • Analyzing data from these organoids (through RNA-seq and ATAC-seq) revealed a progression from pluripotency to retinal specialization, highlighting shifts in gene expression and chromatin structure during early eye field development.
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Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics.

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The cone-rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone-rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high-resolution structures in the published literature for the CRX protein.

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Article Synopsis
  • The CTBP2/RIBEYE gene locus produces diverse isoforms crucial for retina development and helps in coding for various proteins with distinct functions.
  • Through histochemical and sequencing analyses, the study examined how CTBP2 and RIBEYE are expressed at different stages in chicken retinas, revealing CTBP2's broad presence in early developmental stages and RIBEYE's specific expression in photoreceptor cells later.
  • Comparisons between chicken and human retinal development indicate that while the regulation of the CTBP2/RIBEYE locus is similar, it involves different transcription factors in each species.
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The retina is a stratified layer of sensory neurons lining the posterior portion of the eye. In humans, fine detail and color vision are enabled by the macula, a central region of the retina dense in cone photoreceptors (PRs). Achromatic low light and peripheral vision are facilitated by rod PRs found with increasing density outside the macula in the peripheral retina.

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