Genome Sequences and Characteristics of Six Cluster B1 Mycobacteriophages Discovered at Saint Joseph's University.

We report on six new siphoviruses infecting Mycobacterium smegmatis that were isolated from soil samples collected on the campus of Saint Joseph's University, on the western edge of Philadelphia, Pennsylvania. All phages have circularly permuted genomes that are 68,721 to 68,929 bp long, with an average G+C content of 66.4%.

Melanosome Motility in Fish Retinal Pigment Epithelial (RPE) Cells.

Several model systems have been developed to investigate mechanisms and regulation of intracellular organelle motility. The fish retinal pigment epithelial (RPE) cell represents an unusual but simple system for the study of actin-dependent organelle motility. Primary cultures of RPE dissociated from the eye are amenable to motility studies using a simple perfusion chamber and conventional phase contrast microscopy. In vivo, melanin-containing pigment granules (melanosomes) within fish RPE migrate distances up to 100 µm in response to light flux. When sheets of RPE are removed from the eye and dissociated, they attach to the substrate with apical projections extending radially from the central cell body. Melanosomes can be chemically triggered to aggregate or disperse throughout the projections. Melanosome migration in RPE apical projections is dependent on actin filaments and thus renders this model system useful for investigations of actin-dependent organelle motility.

Protein kinase A regulation of pigment granule motility in retinal pigment epithelial cells from fish, Lepomis spp.

Retinomotor movements include elongation and contraction of rod and cone photoreceptors, and mass migration of melanin-containing pigment granules (melanosomes) of the retinal pigment epithelium (RPE) within the eyes of fish, frogs, and other lower vertebrates. Eyes of these animals do not contain dilatable pupils; therefore the repositioning of the rods and cones and a moveable curtain of pigment granules serve to modulate light intensity within the eye. RPE from sunfish (Lepomis spp.) can be isolated from the eye and dissociated into single cells, allowing in vitro studies of the cytoskeletal and regulatory mechanisms of organelle movement. Pigment granule aggregation from distal tips of apical projections into the cell body can be triggered by the application of underivatized cAMP, and dispersion is effected by cAMP washout in the presence of dopamine. While the phenomenon of cAMP-dependent pigment granule aggregation in isolated RPE was described many years ago, whether cAMP acts through the canonical cAMP-PKA pathway to stimulate motility has never been demonstrated. Here, we show that pharmacological inhibition of PKA blocks pigment granule aggregation, and microinjection of protein kinase A catalytic subunit triggers pigment granule aggregation. Treatment with a cAMP agonist that activates the Rap GEF, Epac (Effector protein activated by cAMP), had no effect on pigment granule position. Taken together, these results confirm that cAMP activates RPE pigment granule motility by the canonical cAMP-PKA pathway. Isolated RPE cells labeled with antibodies against PKA RIIα and against PKA-phosphorylated serine/threonine amino acids show diffuse, punctate labeling throughout the RPE cell body and apical projections. Immunoblotting of RPE lysates using the anti-PKA substrate antibody demonstrated seven prominent bands; two bands in particular at 27 and 64 kD showed increased levels of phosphorylation in the presence of cAMP, indicating their phosphorylation could contribute to the pigment granule aggregation mechanism.

Building a laboratory at a Primarily Undergraduate Institution (PUI).

Scientists who are interested in building research programs at primarily-undergraduate institutions (PUIs) have unique considerations compared to colleagues at research-intensive (R1) institutions. Maintaining a research program at a PUI holds unique challenges that should be considered before prospective faculty go on the job market, as they negotiate a job offer, and after they begin a new position. In this article we describe some of the considerations that aspiring and newly hired faculty should keep in mind as they plan out how they will set up a laboratory as a new Principle Investigator (PI) at a PUI.Anyone hoping to start a research program at a PUI should understand both the timeframe of interviews, job offers, and negotiations and the challenges and rewards of working with undergraduate researchers. Once a job is offered, candidates should be aware of the range of negotiable terms that can be part of a start-up package. Space and equipment considerations are also important, and making the most of shared spaces, existing infrastructure, and deals can extend the purchasing power of start-up funds as a new PIs builds their lab. PUIs' focus on undergraduate education and mentorship leads to important opportunities for collaboration, funding, and bringing research projects directly into undergraduate teaching laboratories.A major focus of any new laboratory leader must be on building a productive, equitable, and supportive laboratory community. Equitable onboarding, mentorship plans, and formalized expectations, can all help build a productive and sustainable laboratory research program. However, important considerations about safety, inclusion, student schedules, and a PI's own professional commitments are also extremely important concerns when working with undergraduates in research. A successful research program at a PUI will bring students into meaningful scientific inquiry and requires insights and skills that are often not the focus of scientific training. This article aims to describe the scope of setting up a new laboratory as a way to alleviate some of the burden that new and prospective faculty often feel.

Obtaining a faculty position at a primarily undergraduate institution (PUI).

Scientists who hope to obtain a faculty position at a primarily undergraduate institution (PUI) need a distinct skill set and outlook on their future teaching and research career. To obtain a position at a PUI, candidates should 1) design a strategy for obtaining a faculty position that suits each individual's career goals and aspirations, 2) prepare for the application process, on-campus interview, and contract negotiations, and 3) plan a strategy for the probationary period leading up to tenure and promotion. Given the different types of PUIs, candidates need to consider whether they seek a position that consists of all or mostly all teaching, or both teaching and research. Candidates should educate themselves on the expectations at PUI's, including current thought, practice, and aspirations for science pedagogy, and gain teaching experience prior to seeking a suitable position. If the candidate's goal is a position with both teaching and research, it is important to discuss with the current research mentor what projects the candidate can take with them to their new position. The candidate should also consider what types of projects will be successful with undergraduate student researchers in a PUI research environment. Importantly, candidates should clearly demonstrate a commitment to diversity and inclusion in their teaching, research, and outreach, and application materials should demonstrate this. On interviews, candidates should be knowledgeable about the mission, values, and resources of the institution and how the candidate will contribute to that mission. Once hired, new faculty should discuss a formal or informal mentoring plan during the probationary period that includes peer evaluations on a regular basis, and maintain communication with the department chair or designated mentor regarding teaching, research, and service activities.

Rosette Colonies of Choanoflagellates (Salpingoeca rosetta) Show Increased Food Vacuole Formation Compared with Single Swimming Cells.

Choanoflagellates exist as both single-celled and colonial forms and filter-feed by generating water currents using a single apical flagellum. Hydrodynamic modeling studies have differed in predictions of whether single cells or colonies produce greater fluid flow to enhance feeding, and a recent study reported no increase in feeding efficiency of stalked colonies of choanoflagellates compared with single cells. We report that rosette colonies of Salpingoeca rosetta demonstrate higher rates of food vacuole formation compared with unicellular, slow swimmers.

Melanosome Motility in Fish Retinal Pigment Epithelial (RPE) Cells.

Several model systems have been developed to investigate mechanism and regulation of intracellular organelle motility. The fish retinal pigment epithelial (RPE) cell represents a novel yet simple system for the study of organelle motility. Primary cultures of dissociated RPE cells are easily prepared and amenable to motility studies. In vivo, melanin-containing pigment granules (melanosomes) within fish RPE migrate distances up to 100 µm in response to light flux. When dissociated from the epithelial layer and cultured in vitro, RPE cells attach to the substrate with the apical projections extending radially from the central cell body. Melanosomes can be chemically triggered to aggregate or disperse throughout the projections, and are easily observed using phase contrast microscopy. Melanosome migration in RPE apical projections is dependent on actin filaments, and thus renders this model system useful for investigations of actin-dependent organelle motility.

Comparative genomics of Cluster O mycobacteriophages.

Mycobacteriophages--viruses of mycobacterial hosts--are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages--Corndog, Catdawg, Dylan, Firecracker, and YungJamal--designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange.

Orientation of actin filaments in teleost retinal pigment epithelial cells, and the effect of the lectin, Concanavalin A, on melanosome motility.

Retinal pigment epithelial cells of teleosts contain numerous melanosomes (pigment granules) that exhibit light-dependent motility. In light, melanosomes disperse out of the retinal pigment epithelium (RPE) cell body (CB) into long apical projections that interdigitate with rod photoreceptors, thus shielding the photoreceptors from bleaching. In darkness, melanosomes aggregate through the apical projections back into the CB. Previous research has demonstrated that melanosome motility in the RPE CB requires microtubules, but in the RPE apical projections, actin filaments are necessary and sufficient for motility. We used myosin S1 labeling and platinum replica shadowing of dissociated RPE cells to determine actin filament polarity in apical projections. Actin filament bundles within RPE apical projections are uniformly oriented with barbed ends toward the distal tips. Treatment of RPE cells with the tetravalent lectin, Concanavalin A, which has been shown to suppress cortical actin flow by crosslinking of cell-surface proteins, inhibited melanosome aggregation and stimulated ectopic filopodia formation but did not block melanosome dispersion. The polarity orientation of F-actin in apical projections suggests that a barbed-end directed myosin motor could effect dispersion of melanosomes from the CB into apical projections. Inhibition of aggregation, but not dispersion, by ConA confirms that different actin-dependent mechanisms control these two processes and suggests that melanosome aggregation is sensitive to treatments previously shown to disrupt actin cortical flow.

Melanosome motility in fish retinal pigment epithelial cells.

Several model systems have been developed to investigate intracellular organelle motility. A relatively novel system that is simple but useful for studying mechanisms of organelle motility is the fish retinal pigment epithelial (RPE) cell. Primary cultures of dissociated RPE cells are easily prepared and amenable to organelle motility studies. In vivo, melanin-containing pigment granules (melanosomes) within the RPE migrate long distances in response to light flux. When cultured in vitro, RPE cells attach to the substrate with the apical projections extending radially from the central cell body. Melanosomes can be chemically triggered to aggregate or disperse throughout the projections, and can be easily observed using phase contrast microscopy. Melanosome migration in RPE apical projections is dependent on actin filaments, and thus renders this model system useful for investigations of actin-dependent organelle motility.

Actin-dependent, retrograde motility of surface-attached beads and aggregating pigment granules in dissociated teleost retinal pigment epithelial cells.

Teleost retinal pigment epithelial (RPE) cells contain pigment granules within apical projections which undergo actin-dependent, bi-directional motility. Dissociated RPE cells in culture attach to the substrate and extend apical projections in a radial array from the central cell body. Pigment granules within projections can be triggered to aggregate or disperse by the presence or absence of 1 mM cAMP. Aminated, fluorescent latex beads attached to the dorsal surface of apical projections and moved in the retrograde direction, towards the cell body. Bead rates on RPE cells with aggregating or fully aggregated pigment granules were 2.2 +/- 0.5 and 2.6 +/- 0.2 microm/min (mean +/- SEM), respectively, similar to rates of aggregating (retrograde) pigment granule movement (2.0 +/- 0.4 microm/min). Bead rates were slightly slower on cells with fully dispersed or dispersing pigment granules (1.5 +/- 0.1 and 1.5 +/- 0.4 microm/min). Movements of surface-attached beads and aggregating pigment granules were closely correlated in the distal portions of apical projections, but were more independent of each other in proximal regions of the projections. The actin disrupting drug, cytochalasin D (CD), reversibly halted retrograde bead movements, suggesting that motility of surface-attached particles is actin-dependent. In contrast, the microtubule depolymerizing drug, nocodazole, had no effect on retrograde bead motility. The similar characteristics and actin-dependence of retrograde bead movements and aggregating pigment granules suggest a correlation between these two processes.