Manipulating chromatin architecture in C. elegans.

BACKGROUND: Nucleosome-mediated chromatin compaction has a direct effect on the accessibility of trans-acting activators and repressors to DNA targets and serves as a primary regulatory agent of genetic expression. Understanding the nature and dynamics of chromatin is fundamental to elucidating the mechanisms and factors that epigenetically regulate gene expression. Previous work has shown that there are three types of canonical sequences that strongly regulate nucleosome positioning and thus chromatin accessibility: putative nucleosome-positioning elements, putative nucleosome-repelling sequences, and homopolymeric runs of A/T. It is postulated that these elements can be used to remodel chromatin in C. elegans. Here we show the utility of such elements in vivo, and the extreme efficacy of a newly discovered repelling sequence, PRS-322. RESULTS: In this work, we show that it is possible to manipulate nucleosome positioning in C. elegans solely using canonical and putative positioning sequences. We have not only tested previously described sequences such as the Widom 601, but also have tested additional nucleosome-positioning sequences: the Trifonov sequence, putative repelling sequence-322 (PRS-322), and various homopolymeric runs of A and T nucleotides. CONCLUSIONS: Using each of these types of putative nucleosome-positioning sequences, we demonstrate their ability to alter the nucleosome profile in C. elegans as evidenced by altered nucleosome occupancy and positioning in vivo. Additionally, we show the effect that PRS-322 has on nucleosome-repelling and chromatin remodeling.

Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages.

Bacteriophages are a major force in the evolution of bacteria due to their sheer abundance as well as their ability to infect and kill their hosts and to transfer genetic material. Bacteriophages that infect the Enterobacteriaceae family are of particular interest because this bacterial family contains dangerous animal and plant pathogens. Herein we report the isolation and characterization of two jumbo myovirus Erwinia phages, RisingSun and Joad, collected from apple trees. These two genomes are nearly identical with Joad harboring two additional putative gene products. Despite mass spectrometry data that support the putative annotation, 43% of their gene products have no significant BLASTP hit. These phages are also more closely related to Pseudomonas and Vibrio phages than to published Enterobacteriaceae phages. Of the 140 gene products with a BLASTP hit, 81% and 63% of the closest hits correspond to gene products from Pseudomonas and Vibrio phages, respectively. This relatedness may reflect their ecological niche, rather than the evolutionary history of their host. Despite the presence of over 800 Enterobacteriaceae phages on NCBI, the uniqueness of these two phages highlights the diversity of Enterobacteriaceae phages still to be discovered.

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages.

Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages.

Thyroid gland visualization with 3D/4D ultrasound: integrated hands-on imaging in anatomical dissection laboratory.

PURPOSE: In teaching anatomy, clinical imaging has been utilized to supplement the traditional dissection laboratory promoting education through visualization of spatial relationships of anatomical structures. Viewing the thyroid gland using 3D/4D ultrasound can be valuable to physicians as well as students learning anatomy. The objective of this study was to investigate the perceptions of first-year medical students regarding the integration of 3D/4D ultrasound visualization of spatial anatomy during anatomical education. METHODS: 108 first-year medical students were introduced to 3D/4D ultrasound imaging of the thyroid gland through a detailed 20-min tutorial taught in small group format. Students then practiced 3D/4D ultrasound imaging on volunteers and donor cadavers before assessment through acquisition and identification of thyroid gland on at least three instructor-verified images. A post-training survey was administered assessing student impression. RESULTS: All students visualized the thyroid gland using 3D/4D ultrasound. Students revealed 88.0% strongly agreed or agreed 3D/4D ultrasound is useful revealing the thyroid gland and surrounding structures and 87.0% rated the experience "Very Easy" or "Easy", demonstrating benefits and ease of use including 3D/4D ultrasound in anatomy courses. When asked, students felt 3D/4D ultrasound is useful in teaching the structure and surrounding anatomy of the thyroid gland, they overwhelmingly responded "Strongly Agree" or "Agree" (90.2%). CONCLUSION: This study revealed that 3D/4D ultrasound was successfully used and preferred over 2D ultrasound by medical students during anatomy dissection courses to accurately identify the thyroid gland. In addition, 3D/4D ultrasound may nurture and further reinforce stereostructural spatial relationships of the thyroid gland taught during anatomy dissection.