CD8+ T cell targeting of tumor antigens presented by HLA-E.

The nonpolymorphic major histocompatibility complex E (MHC-E) molecule is up-regulated on many cancer cells, thus contributing to immune evasion by engaging inhibitory NKG2A/CD94 receptors on NK cells and tumor-infiltrating T cells. To investigate whether MHC-E expression by cancer cells can be targeted for MHC-E-restricted T cell control, we immunized rhesus macaques (RM) with rhesus cytomegalovirus (RhCMV) vectors genetically programmed to elicit MHC-E-restricted CD8+ T cells and to express established tumor-associated antigens (TAAs) including prostatic acidic phosphatase (PAP), Wilms tumor-1 protein, or Mesothelin. T cell responses to all three tumor antigens were comparable to viral antigen-specific responses with respect to frequency, duration, phenotype, epitope density, and MHC restriction. Thus, CMV-vectored cancer vaccines can bypass central tolerance by eliciting T cells to noncanonical epitopes. We further demonstrate that PAP-specific, MHC-E-restricted CD8+ T cells from RhCMV/PAP-immunized RM respond to PAP-expressing HLA-E+ prostate cancer cells, suggesting that the HLA-E/NKG2A immune checkpoint can be exploited for CD8+ T cell-based immunotherapies.

Morphogenesis of bacterial colonies in polymeric environments.

Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, lab studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.

Response of treatment-naive brain metastases to stereotactic radiosurgery.

With improvements in survival for patients with metastatic cancer, long-term local control of brain metastases has become an increasingly important clinical priority. While consensus guidelines recommend surgery followed by stereotactic radiosurgery (SRS) for lesions >3 cm, smaller lesions (≤3 cm) treated with SRS alone elicit variable responses. To determine factors influencing this variable response to SRS, we analyzed outcomes of brain metastases ≤3 cm diameter in patients with no prior systemic therapy treated with frame-based single-fraction SRS. Following SRS, 259 out of 1733 (15%) treated lesions demonstrated MRI findings concerning for local treatment failure (LTF), of which 202 /1733 (12%) demonstrated LTF and 54/1733 (3%) had an adverse radiation effect. Multivariate analysis demonstrated tumor size (>1.5 cm) and melanoma histology were associated with higher LTF rates. Our results demonstrate that brain metastases ≤3 cm are not uniformly responsive to SRS and suggest that prospective studies to evaluate the effect of SRS alone or in combination with surgery on brain metastases ≤3 cm matched by tumor size and histology are warranted. These studies will help establish multi-disciplinary treatment guidelines that improve local control while minimizing radiation necrosis during treatment of brain metastasis ≤3 cm.

The role of implementing instructional design principles on learner experience with training in current good manufacturing practices (cGMP).

INTRODUCTION: The objective of the study was to assess if improvement of the learner experience could be achieved through the use of instructional design strategies in current Good Manufacturing Practices (cGMP) training. This is a novel application in a topic that is known to be boring but is critical to ensuring patient safety. METHODS: An experimental randomized controlled repeated measures cross-over design was utilized in a sample of pharmacy students to determine the effect of an intervention training strategy (which utilized a mix of strategies including weeding, signaling, use of multimedia, and optimized space and type) on the learner experience (Evaluation, Overall Satisfaction, Perceived Knowledge, and Future Recommendation) compared with a control. RESULTS: The sample of 52 pharmacy students that participated evaluated the intervention training strategy with higher scores than the control, with better overall satisfaction, perceived knowledge, and future recommendation scores than the control training strategy. Thus, an apparent effect which resulted from the use of instructional design strategies was seen for all learner experience variables (p < .01). CONCLUSION: Improvement in the learner experience can be achieved by using instructional design strategies in cGMP training. This indicates that similar results could be obtained in other topics where such techniques have not yet been applied.

Integrated curriculum in the United States pharmacy programs.

INTRODUCTION: In the last decade, significant changes in pharmaceutical sciences have influenced the delivery of pharmacy education in Pharmacy programs. Integrated curriculum is one such method considered. We aimed to describe the perceived level of integrated curriculum among PharmD programs in the US. METHODS: From October 26th, 2021, until January 18th, 2022, faculty administrators across 138 US pharmacy colleges were surveyed. Data was collected regarding each program's perceived curriculum integration and assessment integration. Characteristics of each college, including region and the type of school (public/private), were obtained from the PharmCAS website. Programs were categorized into high-integration and low-integration groups for analysis purposes. Descriptive and comparative analysis by the level of curriculum integration was performed. RESULTS: Overall, 60 colleges completed surveys (participation rate = 43.48%). Most schools were from the South region (38.33%) and public colleges (53.33%). The average perceived curriculum integration was 45% (SD = 23.69), while the average perceived assessment integration was 36% (SD = 25.52). Pharmacy practice [clinical sciences] (76.67%) was the most common discipline considered for integration, and the social and administrative sciences (21.67%) was the discipline least commonly considered for integration. Case-based learning (95%) was the most common pedagogy strategy to integrate knowledge from different disciplines. CONCLUSIONS: Integrated curriculum implementation in the US PharmD programs varied across colleges. While most programs integrated their clinical practice courses, social and administrative sciences was the course least commonly integrated. Very limited progress in assessment integration was perceived.

Interplay between environmental yielding and dynamic forcing modulates bacterial growth.

Many bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly tunable structural and rheological properties, under different amounts of external forcing imposed by mechanical shaking, and in both aerobic and anaerobic conditions. Our experiments establish a general principle: that the balance between the yield stress of the environment that the cells inhabit, σy, and the external stress imposed on the environment, σ, modulates bacterial growth by altering transport of essential nutrients to the cells. In particular, when σy<σ, the environment is easily fluidized and mixed over large scales, providing nutrients to the cells and sustaining complete cellular growth. By contrast, when σy>σ, the elasticity of the environment suppresses large-scale fluid mixing, limiting nutrient availability and arresting cellular growth. Our work thus reveals a new mechanism, beyond effects that change cellular behavior via local forcing, by which the rheology of the environment may modulate microbial physiology in diverse natural and industrial settings.

Patterns of immunotherapy utilization for non-small cell lung cancer in Texas pre- and post-regulatory approval.

PURPOSE: Immunotherapy has shown remarkable benefits for non-small cell lung cancer (NSCLC) since approved by the US Food and Drug Administration (FDA). Texas, however, ranks below the national average in access to treatment for NSCLC. This retrospective cohort study assessed first-line immunotherapy treatment patterns and associated factors pre- and post-FDA approval in Texas. METHODS: Patients ≥18 years diagnosed with NSCLC from the Texas Cancer Registry database (2011-2018) and were stratified into pre- and post-FDA approval era. The rates of immunotherapy utilization were examined, and the average annual percent change (AAPC) in immunotherapy utilization across patient subgroups was compared. Multivariable logistic regression was used to identify associations of patient characteristics with immunotherapy utilization for patients with metastatic- and all-stage NSCLC. RESULTS: A total of 13,501 and 9509 patients with NSCLC were identified in pre-post-approval periods, respectively. Post-approval, immunotherapy utilization increased from 1.7 to 13.0%, and AAPC from 54.8 to 82.7%. Pre-approval, patients living in a county with ≥20% of households below the poverty level were less likely to receive immunotherapy (OR = 0.73, 95% CI = 0.61-0.94) while patients with private insurance were more likely to receive immunotherapy (OR = 1.56, 95% CI = 1.10-2.23). Post-approval, socioeconomic disparities were more prominent (10-19.9 and ≥20% of households below the poverty level: OR = 0.77, 95% CI = 0.66-0.90 and OR = 0.71, 95% CI = 0.60-0.86, respectively). Patients with metastatic NSCLC showed similar patterns of socioeconomic disparities pre- and post-approval. CONCLUSIONS: Our findings suggest that patients' socioeconomic status hinders immunotherapy utilization for NSCLC in Texas. This emphasizes the need for state health policy reforms such as Medicaid expansion and tailored cancer care strategies.

3D Printing Bacteria to Study Motility and Growth in Complex 3D Porous Media.

Bacteria are ubiquitous in complex three-dimensional (3D) porous environments, such as biological tissues and gels, and subsurface soils and sediments. However, the majority of previous work has focused on studies of cells in bulk liquids or at flat surfaces, which do not fully recapitulate the complexity of many natural bacterial habitats. Here, this gap in knowledge is addressed by describing the development of a method to 3D-print dense colonies of bacteria into jammed granular hydrogel matrices. These matrices have tunable pore sizes and mechanical properties; they physically confine the cells, thus supporting them in 3D. They are optically transparent, allowing for direct visualization of bacterial spreading through their surroundings using imaging. As a proof of this principle, here, the capability of this protocol is demonstrated by 3D printing and imaging non-motile and motile Vibro cholerae, as well as non-motile Escherichia coli, in jammed granular hydrogel matrices with varying interstitial pore sizes.

Intraoperative language mapping guided by real-time visualization of gamma band modulation electrocorticograms: Case report and proof of concept.

Background: Electrocorticography (ECoG) language mapping is often performed extraoperatively, frequently involves offline processing, and relationships with direct cortical stimulation (DCS) remain variable. We sought to determine the feasibility and preliminary utility of an intraoperative language mapping approach guided by real-time visualization of electrocorticograms. Methods: A patient with astrocytoma underwent awake craniotomy with intraoperative language mapping, utilizing a dual iPad stimulus presentation system coupled to a real-time neural signal processing platform capable of both ECoG recording and delivery of DCS. Gamma band modulations in response to 4 language tasks at each electrode were visualized in real-time. Next, DCS was conducted for each neighboring electrode pair during language tasks. Results: All language tasks resulted in strongest heat map activation at an electrode pair in the anterior to mid superior temporal gyrus. Consistent speech arrest during DCS was observed for Object and Action naming tasks at these same electrodes, indicating good correspondence with ECoG heat map recordings. This region corresponded well with posterior language representation via preoperative functional MRI. Conclusions: Intraoperative real-time visualization of language task-based ECoG gamma band modulation is feasible and may help identify targets for DCS. If validated, this may improve the efficiency and accuracy of intraoperative language mapping.

Obstructed swelling and fracture of hydrogels.

Obstructions influence the growth and expansion of bodies in a wide range of settings-but isolating and understanding their impact can be difficult in complex environments. Here, we study obstructed growth/expansion in a model system accessible to experiments, simulations, and theory: hydrogels swelling around fixed cylindrical obstacles with varying geometries. When the obstacles are large and widely-spaced, hydrogels swell around them and remain intact. In contrast, our experiments reveal that when the obstacles are narrow and closely-spaced, hydrogels fracture as they swell. We use finite element simulations to map the magnitude and spatial distribution of stresses that build up during swelling at equilibrium in a 2D model, providing a route toward predicting when this phenomenon of self-fracturing is likely to arise. Applying lessons from indentation theory, poroelasticity, and nonlinear continuum mechanics, we also develop a theoretical framework for understanding how the maximum principal tensile and compressive stresses that develop during swelling are controlled by obstacle geometry and material parameters. These results thus help to shed light on the mechanical principles underlying growth/expansion in environments with obstructions.

Circulating tumor DNA and radiological tumor volume identify patients at risk for relapse with resected, early-stage non-small-cell lung cancer.

BACKGROUND: Predicting relapse and overall survival (OS) in early-stage non-small-cell lung cancer (NSCLC) patients remains challenging. Therefore, we hypothesized that detection of circulating tumor DNA (ctDNA) can identify patients with increased risk of relapse and that integrating radiological tumor volume measurement along with ctDNA detectability improves prediction of outcome. PATIENTS AND METHODS: We analyzed 366 serial plasma samples from 85 patients who underwent surgical resections and assessed ctDNA using a next-generation sequencing liquid biopsy assay, and measured tumor volume using a computed tomography-based three-dimensional annotation. RESULTS: Our results showed that patients with detectable ctDNA at baseline or after treatment and patients who did not clear ctDNA after treatment had a significantly worse clinical outcome. Integrating radiological analysis allowed the stratification in risk groups prognostic of clinical outcome as confirmed in an independent cohort of 32 patients. CONCLUSIONS: Our findings suggest ctDNA and radiological monitoring could be valuable tools for guiding follow-up care and treatment decisions for early-stage NSCLC patients.

Subependymomas of the fourth ventricle: To operate or not to operate?

BACKGROUND: There is a paucity of literature regarding the clinical characteristics and management of subependymomas of the fourth ventricle due to their rarity. Here, we describe the operative and non-operative management and outcomes of patients with such tumors. METHODS: This retrospective single-institution case series was gathered after Institutional Review Board (IRB) approval. Patients diagnosed with a subependymoma of the fourth ventricle between 1993 and 2021 were identified. Clinical, radiology and pathology reports along with magnetic resonance imaging (MRI) images were reviewed. RESULTS: Patients identified (n = 20), showed a male predominance (n = 14). They underwent surgery (n = 9) with resection and histopathological confirmation of subependymoma or were followed with imaging surveillance (n = 11). The median age at diagnosis was 51.5 years. Median tumor volume for the operative cohort was 8.64 cm3 and median length of follow-up was 65.8 months. Median tumor volume for the non-operative cohort was 0.96 cm3 and median length of follow-up was 78 months. No tumor recurrence post-resection was noted in the operative group, and no tumor growth from baseline was noted in the non-operative group. Most patients (89 %) in the operative group had symptoms at diagnosis, all of which improved post-resection. No patients were symptomatic in the non-operative group. CONCLUSIONS: Surgical resection is safe and is associated with alleviation of presenting symptoms in patients with large tumors. Observation and routine surveillance are warranted for smaller, asymptomatic tumors.

Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift.

Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.

Interfacial morphodynamics of proliferating microbial communities.

In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains-which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.

Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass.

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33-9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032-0.131 (g/g) and lipid contents were 13.5-53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature. SUMMARY: The yeast Rhodotorula toruloides was used to produce oil using sugars extracted from a bioenergy grass.

Pattern formation by bacteria-phage interactions.

The interactions between bacteria and phages-viruses that infect bacteria-play critical roles in agriculture, ecology, and medicine; however, how these interactions influence the spatial organization of both bacteria and phages remain largely unexplored. Here, we address this gap in knowledge by developing a theoretical model of motile, proliferating bacteria that aggregate via motility-induced phase separation (MIPS) and encounter phage that infect and lyse the cells. We find that the non-reciprocal predator-prey interactions between phage and bacteria strongly alter spatial organization, in some cases giving rise to a rich array of finite-scale stationary and dynamic patterns in which bacteria and phage coexist. We establish principles describing the onset and characteristics of these diverse behaviors, thereby helping to provide a biophysical basis for understanding pattern formation in bacteria-phage systems, as well as in a broader range of active and living systems with similar predator-prey or other non-reciprocal interactions.

Tough and Recyclable Phase-Separated Supramolecular Gels via a Dehydration-Hydration Cycle.

Hydrogels are compelling materials for emerging applications including soft robotics and autonomous sensing. Mechanical stability over an extensive range of environmental conditions and considerations of sustainability, both environmentally benign processing and end-of-life use, are enduring challenges. To make progress on these challenges, we designed a dehydration-hydration approach to transform soft and weak hydrogels into tough and recyclable supramolecular phase-separated gels (PSGs) using water as the only solvent. The dehydration-hydration approach led to phase separation and the formation of domains consisting of strong polymer-polymer interactions that are critical for forming PSGs. The phase-separated segments acted as robust, physical cross-links to strengthen PSGs, which exhibited enhanced toughness and stretchability in its fully swollen state. PSGs are not prone to overswelling or severe shrinkage in wet conditions and show environmental tolerance in harsh conditions, e.g., solutions with pH between 1 and 14. Finally, we demonstrate the use of PSGs as strain sensors in air and aqueous environments.

Liquid-liquid phase separation within fibrillar networks.

Complex fibrillar networks mediate liquid-liquid phase separation of biomolecular condensates within the cell. Mechanical interactions between these condensates and the surrounding networks are increasingly implicated in the physiology of the condensates and yet, the physical principles underlying phase separation within intracellular media remain poorly understood. Here, we elucidate the dynamics and mechanics of liquid-liquid phase separation within fibrillar networks by condensing oil droplets within biopolymer gels. We find that condensates constrained within the network pore space grow in abrupt temporal bursts. The subsequent restructuring of condensates and concomitant network deformation is contingent on the fracture of network fibrils, which is determined by a competition between condensate capillarity and network strength. As a synthetic analog to intracellular phase separation, these results further our understanding of the mechanical interactions between biomolecular condensates and fibrillar networks in the cell.

Chemotactic Motility-Induced Phase Separation.

Collectives of actively moving particles can spontaneously separate into dilute and dense phases-a fascinating phenomenon known as motility-induced phase separation (MIPS). MIPS is well-studied for randomly moving particles with no directional bias. However, many forms of active matter exhibit collective chemotaxis, directed motion along a chemical gradient that the constituent particles can generate themselves. Here, using theory and simulations, we demonstrate that collective chemotaxis strongly competes with MIPS-in some cases, arresting or completely suppressing phase separation, or in other cases, generating fundamentally new dynamic instabilities. We establish principles describing this competition, thereby helping to reveal and clarify the rich physics underlying active matter systems that perform chemotaxis, ranging from cells to robots.