Optimized Red-Absorbing Dyes for Imaging and Sensing.

Rhodamine dyes are excellent scaffolds for developing a broad range of fluorescent probes. A key property of rhodamines is their equilibrium between a colorless lactone and fluorescent zwitterion. Tuning the lactone-zwitterion equilibrium constant (KL-Z) can optimize dye properties for specific biological applications. Here, we use known and novel organic chemistry to prepare a comprehensive collection of rhodamine dyes to elucidate the structure-activity relationships that govern KL-Z. We discovered that the auxochrome substituent strongly affects the lactone-zwitterion equilibrium, providing a roadmap for the rational design of improved rhodamine dyes. Electron-donating auxochromes, such as julolidine, work in tandem with fluorinated pendant phenyl rings to yield bright, red-shifted fluorophores for live-cell single-particle tracking (SPT) and multicolor imaging. The N-aryl auxochrome combined with fluorination yields red-shifted Förster resonance energy transfer (FRET) quencher dyes useful for creating a new semisynthetic indicator to sense cAMP using fluorescence lifetime imaging microscopy (FLIM). Together, this work expands the synthetic methods available for rhodamine synthesis, generates new reagents for advanced fluorescence imaging experiments, and describes structure-activity relationships that will guide the design of future probes.

Expanding Staff Voice in Protected Area Management Effectiveness Assessments within Kenya's Maasai Mara National Reserve.

The concept of protected areas (PA) is one of the most widely used policy tools for biodiversity conservation including habitat and wildlife protection. Despite the importance and emphasis placed on protected area management, biodiversity is still in decline and more species are in danger of extinction. Some analyses have indicated that more than 40% of protected areas are poorly managed. To improve management effectiveness, the inclusion of diverse stakeholder information in articulating management strategies has been strongly encouraged; however, stakeholder involvement is often poorly integrated, and an opportunity granted only to select stakeholder groups, with PA staff, especially at lower organizational levels, minimally involved. Further, protected area management effectiveness (PAME) assessments are most frequently used as an aggregated outcome measure of effectiveness but these data should also inform management practice. Thus, for PA managers to obtain a greater understanding of issues impacting their effectiveness, they would benefit from including the voices of staff at all working levels. Therefore, the purpose of this investigation was to survey 135 wardens and rangers at all organizational levels from the two administrative sectors of Maasai Mara National Reserve to determine their perceptions of management effectiveness and to determine if significant differences existed across staff levels and administrative sectors. Significant differences were found to exist across staff levels and administrative authorities supporting the need for expanded staff voice in establishing effective PA management plans.

Computed Tomography Imaging Patterns of Sinonasal Inverted Papillomas: Comparison of Primary and Recurrent Disease.

OBJECTIVE: To analyze clinical and radiographic features that may impact the rate of focal hyperostosis (FH) on computed tomography (CT) for primary and recurrent sinonasal inverted papillomas (IPs) as well as highlight factors that may affect concordance between FH and IP true attachment point (TAP). METHODS: All IPs resected between 2006 and 2022 were retrospectively reviewed. CTs were read by a neuroradiologist blinded to operative details. IP with malignancy was excluded. Operative reports and long-term follow-up data were evaluated. RESULTS: Of 92 IPs, 60.1% had FH, 25% had no CT bony changes, and 20.7% were revision cases. The recurrence rate for rhinologists was 10.5% overall and 7.3% for primary IPs. Primary and revision IPs had a similar rate of FH (63% vs. 52.6%; p = 0.646) and FH-TAP agreement (71.7% vs. 90%; p = 0.664). Nasal cavity IPs, especially with septal attachment, were more likely to lack bony changes on CT (57.1%) compared to other subsites (p = 0.018). Recurrent tumors were 16 mm larger on average (55 mm vs. 39 mm; p = 0.008). FH (75.0% vs. 60.9%; p = 0.295), FH-TAP concordance (91.7% vs. 74.4%; p = 0.094), and secondary IP (18.8% vs. 20.3%; p = 0.889) rates were similar between recurrent and nonrecurrent tumors. CONCLUSION: Primary and revision IPs have a similar rate of FH and FH-TAP agreement. Nasal cavity IPs are less likely to exhibit bony CT changes. Lower recurrence was associated with smaller size and fellowship training but not multiple TAPs, revision, FH absence, or FH-TAP discordance. LEVEL OF EVIDENCE: 3 Laryngoscope, 134:1591-1596, 2024.

Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.

In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.

Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers.

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.

Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers.

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.

A series of spontaneously blinking dyes for super-resolution microscopy.

Spontaneously blinking fluorophores permit the detection and localization of individual molecules without reducing buffers or caging groups, thus simplifying single-molecule localization microscopy (SMLM). The intrinsic blinking properties of such dyes are dictated by molecular structure and modulated by environment, which can limit utility. We report a series of tuned spontaneously blinking dyes with duty cycles that span two orders of magnitude, allowing facile SMLM in cells and dense biomolecular structures.

A prime editor mouse to model a broad spectrum of somatic mutations in vivo.

Genetically engineered mouse models only capture a small fraction of the genetic lesions that drive human cancer. Current CRISPR-Cas9 models can expand this fraction but are limited by their reliance on error-prone DNA repair. Here we develop a system for in vivo prime editing by encoding a Cre-inducible prime editor in the mouse germline. This model allows rapid, precise engineering of a wide range of mutations in cell lines and organoids derived from primary tissues, including a clinically relevant Kras mutation associated with drug resistance and Trp53 hotspot mutations commonly observed in pancreatic cancer. With this system, we demonstrate somatic prime editing in vivo using lipid nanoparticles, and we model lung and pancreatic cancer through viral delivery of prime editing guide RNAs or orthotopic transplantation of prime-edited organoids. We believe that this approach will accelerate functional studies of cancer-associated mutations and complex genetic combinations that are challenging to construct with traditional models.

Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.

In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we developed an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrated that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacted nucleosome diffusive properties in a manner that was dependent on local chromatin density and supportive of a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Our results reveal that nuclear heterogeneity arises from both active and passive process and highlights the need to account for different organizational principals when modeling different chromatin environments.

A nationwide analysis of salvage surgery for laryngeal cancer in the elderly.

BACKGROUND: We aim to describe outcomes of elderly patients undergoing salvage surgery for laryngeal cancer and to characterize the interplay of age with various other factors in this growing population. METHODS: Using the National Cancer Database, we identified cases of salvage laryngectomy in patients who failed chemoradiation. An age cutoff of 70 years was used to separate subjects into two groups. Various factors were compared. RESULTS: Of the 825 patients included, 166 (20.1%) were elderly. Elderly patients had worse overall survival (p = 0.001), higher 30-day and 90-day mortality (p = 0.006, p < 0.001), and a longer length of stay (LOS) (p = 0.015). LOS over 1 week was associated with worse survival (p = 0.032). CONCLUSION: Elderly patients had worse overall perioperative survival than their younger counterparts. LOS and 30-day readmissions were associated with higher risk of mortality in this group. We provide a contemporary set of relevant information for head and neck cancer providers to consider in this growing population.

Causes of Cancer Re-Admissions: A Patient-Centered Approach.

PURPOSE: Patients with a cancer diagnosis have a high risk of re-admission during the 30 days after discharge. Clinicians, payers, and patients consider this to be an indicator of care quality. The causes of re-admission remain poorly understood. Retrospective chart reviews, used in most re-admission research, provide limited information regarding the causes of, and methods to reduce, re-admissions. This project sought to elicit the insights of those most affected by re-admission: the patients themselves. METHODS: We interviewed patients with cancer who were re-admitted to 2 urban teaching hospitals when they were hospitalized during their second admission. Trained interviewers used a semistructured interview guide to gather information on events just before the second admission, the patients' understanding of the cause of re-admission, and the patients' views about their readiness for discharge at the previous admission. Interviews were transcribed and analyzed, and themes were identified and explored. RESULTS: Three major themes were identified. First, most patients saw their re-admission as caused by problems that could not be treated in an outpatient setting. Second, the patients felt that they did not have sufficient resources at home to manage their care. Furthermore, the patients did not see the outpatient care team as a resource that they could call on for assistance. As a result, most of the decisions to return to the hospital were made by the patients themselves. CONCLUSION: The decision that leads to re-admission often happens at home, in response to unmanageable needs. Strengthening the bond between the care team and the patient, with the aim of providing care in the most appropriate setting, could decrease re-admissions in patients with cancer. Possible interventions include home visits, enhanced discharge planning, and telehealth services.