A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms

Introduction: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus—hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence. Objectives: To explore the interaction, we used a novel GC-Orbitrap-based mass spectrometer, the Q Exactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards. Methods: Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed using the new instrument in addition to the fresh and spent bacterial growth media. Results: The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. Untargeted analysis resulted in the detection of 465 features from fresh and spent medium and 405 from biofilm samples. Three significantly changing compounds that matched to high scoring library fragment patterns were chosen for validation. Conclusion: Evaluation of the results demonstrates that the Q Exactive GC is suitable for metabolomics analysis using a targeted/untargeted methodology. Many of the results were as expected: e.g. rapid consumption of glucose and fructose from the medium regardless of the cell type. Modulation of sugar-phosphate levels also suggest that the pentose phosphate pathway could be enhanced in the cells from co-cultured biofilms. Untargeted metabolomics results suggested significant production of cell-wall biosynthesis components and the consumption of non-proteinaceous amino-acids

Spirituality, Faith, and Mild Alzheimer\u27s Disease

There is some evidence for a positive association between spirituality, cognitive, and behavioral functioning in people with Alzheimer’s disease (AD). However, to our knowledge there is no published data to date that provides an explanatory model for these findings. Twenty-eight individuals with mild AD received in-depth interviews and measures of cognitive, behavioral, emotional, and spiritual functioning to gain insight into this question in this mixed methods study. Findings revealed that people with mild AD can actively engage in meaningful discussion about how spirituality influences their experience of living with AD; that they remain deeply devoted to a relationship with the transcendent (i.e., God, higher power, spirit) and their spiritual communities; that they value and benefit from the sacred aspects of their day-to-day lives; and that their core spiritual values, beliefs, and practices can be activated to help them adapt to the uncertainty of living with AD. Additionally, persons with AD who are experiencing spiritual struggle tend to experience a greater degree of anxiety, depression, and behavioral changes as compared to those who do not, suggesting that spiritual struggle is a risk factor for poorer outcomes in this population. Implications for future research, clinical practice, and community care are provided including how researchers and clinicians can effectively adapt traditional measures of spirituality for use with this population; the importance of integrating spirituality into the assessment and treatment of people with AD; and the role spiritual communitie

Doc’Apella: A Vocal Performance Group Designed to Reduce Stress And Prevent Burnout Among Medical and Health Sciences Students

Introduction: Burnout is common among health professions trainees characterized by emotional exhaustion induced by repeated stressors. Although traditional stress management activities to promote wellness are effective in reducing stress short-term, alternative approaches are needed with the potential for long-term impact. To address burnout among students at the University of Nebraska Medical Center (UNMC), a vocal group was formed to provide a creative outlet. The purpose of this study was to determine the students’ motivation for joining Doc’Apella and assess the impact on burnout. Methods: Students enrolled in a health sciences program were invited to participate during the 2018-19 academic year (August-May). Two volunteer students arranged the music, recorded individual practice tracks, and directed the group during rehearsals two nights/week from 5:30-6:30. Group members selected arrangements and performed in a variety of settings. At the end of the year, participants were invited to complete an anonymous online survey. Results: Of the 98 students on the roster, 18 (18.4%) responded to the survey. Participants included medical students (n = 9, 50.0%), three graduate students (16.7%), two public health students (11.1%), one pharmacy student (5.5%), and three classified as “other” (16.7%). Nine (50.0%) indicated the aspect of the group that was MOST important was “escaping my stress or frustration with a creative activity.” Thirteen (72.2%) felt Doc’Apella was very or extremely beneficial to their “own sense of wellbeing” and 94.4% (n = 17) reported Doc’Apella “helped reduce stress and burnout” somewhat or very much. Conclusion: Creating music with others may provide an effective way for medical trainees to not only to express creative energy but also to connect with others across health professions. Although the results support structured creative activities to reduce stress and burnout, a large-scale study is needed will strengthen empirical evidence and highlight the impact for health professions trainees

PAI-1 is a Critical Upstream Regulator of the TGF-β1/EGF-Induced Invasive Phenotype in Mutant p53 Human Cutaneous Squamous Cell Carcinoma

The emergence of highly aggressive subtypes of human cutaneous squamous cell carcinoma (SCC) often reflects increased autocrine/paracrine TGF-β synthesis and epidermal growth factor receptor (EGFR) amplification. Cooperative TGF-β/EGFR signaling promotes cell migration and induces expression of both proteases and protease inhibitors that regulate stromal remodeling resulting in acquisition of an invasive phenotype. TGF-β1+EGF stimulation increases the production of several matrix metalloproteinases (MMPs) in human SCC. Among the most prominent is MMP-10 which is known to be elevated in SCC in situ. Activation of stromal plasminogen appears to be critical in triggering downstream MMP activity. Paradoxically, PAI-1, the major physiological inhibitor of plasmin generation, is also up-regulated under these conditions and is an early event in progression of incipient epidermal SCC. A model is proposed in which TGF-β1+EGF-dependent MMP-10 elevation directs focalized matrix remodeling events that promote epithelial cell plasticity and tissue invasion. Increased PAI-1 expression serves to temporally and spatially modulate plasmin-initiated pericellular proteolysis, further facilitating epithelial invasive potential. Defining the complex signaling mechanisms that maintain this elegant balance is critical to developing potential therapeutics for the treatment of human cutaneous malignancies

PAI-1 Regulates the Invasive Phenotype in Human Cutaneous Squamous Cell Carcinoma

The emergence of highly aggressive subtypes of human cutaneous squamous cell carcinoma (SCC) often reflects increased autocrine/paracrine TGF-β synthesis and epidermal growth factor receptor (EGFR) amplification. Cooperative TGF-β/EGFR signaling promotes cell migration and induces expression of both proteases and protease inhibitors that regulate stromal remodeling resulting in the acquisition of an invasive phenotype. In one physiologically relevant model of human cutaneous SCC progression, TGF-β1+EGF stimulation increases the production of several matrix metalloproteinases (MMPs), among the most prominent of which is MMP-10—an MMP known to be elevated in SCC in situ. Activation of stromal plasminogen appears to be critical in triggering downstream MMP activity. Paradoxically, PAI-1, the major physiological inhibitor of plasmin generation, is also upregulated under these conditions and is an early event in progression of incipient epidermal SCC. One testable hypothesis proposes that TGF-β1+EGF-dependent MMP-10 elevation directs focalized matrix remodeling events that promote epithelial cell plasticity and tissue invasion. Increased PAI-1 expression serves to temporally and spatially modulate plasmin-initiated pericellular proteolysis, further facilitating epithelial invasive potential. Defining the complex signaling and transcriptional mechanisms that maintain this delicate balance is critical to developing targeted therapeutics for the treatment of human cutaneous malignancies

Associations among salivary cortisol, melatonin, catecholamines, sleep quality and stress in women with breast cancer and healthy controls

Dysregulations in several biological systems in breast cancer patients have been reported, including abnormalities in endocrine and sympathetic nervous system indices, as well as psychological disturbances and sleep disorders. The purpose of this exploratory study was to compare women with breast cancer to healthy control women on measures of salivary cortisol, urinary catecholamines, overnight urinary melatonin, and self-reported sleep quality, symptoms of stress, depression, anxiety and mood disturbance, to determine if discernable patterns of dysregulations across systems were apparent. Thirty-three women were tested in each group, with an average age of approximately 52 years, primarily Caucasian and welleducated. Forty percent of the women with breast cancer had stage 2 disease and they were an average of 1.36 years post-diagnosis. Women with breast cancer had significantly higher levels of disturbance on all the psychological indices, but there were no differences between groups on any of the biological measures, with the exception that the control women had higher dopamine values than the participants with breast cancer. None of the psychological scores were correlated with the biological measures. These results are consistent with other studies of early-stage breast cancer and highlight the importance of considering disease characteristics when investigating endocrine and sympathetic nervous system functioning. KEY WORDS: breast cancer; cortisol; melatonin; catecholamines; stress; depression; anxiety. Women with breast cancer have been documented to have dysregulation in several important circadian systems, including hormonal, sleep and autonomic rhythm

A Francisella tularensis Live Vaccine Strain That Improves Stimulation of Antigen-Presenting Cells Does Not Enhance Vaccine Efficacy

Vaccination is a proven strategy to mitigate morbidity and mortality of infectious diseases. The methodology of identifying and testing new vaccine candidates could be improved with rational design and in vitro testing prior to animal experimentation. The tularemia vaccine, Francisella tularensis live vaccine strain (LVS), does not elicit complete protection against lethal challenge with a virulent type A Francisella strain. One factor that may contribute to this poor performance is limited stimulation of antigen-presenting cells. In this study, we examined whether the interaction of genetically modified LVS strains with human antigen-presenting cells correlated with effectiveness as tularemia vaccine candidates. Human dendritic cells infected with wild-type LVS secrete low levels of proinflammatory cytokines, fail to upregulate costimulatory molecules, and activate human T cells poorly in vitro. One LVS mutant, strain 13B47, stimulated higher levels of proinflammatory cytokines from dendritic cells and macrophages and increased costimulatory molecule expression on dendritic cells compared to wild type. Additionally, 13B47-infected dendritic cells activated T cells more efficiently than LVS-infected cells. A deletion allele of the same gene in LVS displayed similar in vitro characteristics, but vaccination with this strain did not improve survival after challenge with a virulent Francisella strain. In vivo, this mutant was attenuated for growth and did not stimulate T cell responses in the lung comparable to wild type. Therefore, stimulation of antigen-presenting cells in vitro was improved by genetic modification of LVS, but did not correlate with efficacy against challenge in vivo within this model system

Measurement of the Neutron Lifetime by Counting Trapped Protons in a Cold Neutron Beam

A measurement of the neutron lifetime $\tau_{n}$ performed by the absolute counting of in-beam neutrons and their decay protons has been completed. Protons confined in a quasi-Penning trap were accelerated onto a silicon detector held at a high potential and counted with nearly unit efficiency. The neutrons were counted by a device with an efficiency inversely proportional to neutron velocity, which cancels the dwell time of the neutron beam in the trap. The result is $\tau_{n} = (886.6\pm1.2{\rm [stat]}\pm3.2{\rm [sys]})$ s, which is the most precise measurement of the lifetime using an in-beam method. The systematic uncertainty is dominated by neutron counting, in particular the mass of the deposit and the $^{6}$Li({\it{n,t}}) cross section. The measurement technique and apparatus, data analysis, and investigation of systematic uncertainties are discussed in detail.Comment: 71 pages, 20 figures, 9 tables; submitted to PR

Bayesian correlated clustering to integrate multiple datasets

Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct – but often complementary – information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured via parameters that describe the agreement among the datasets. Results: Using a set of 6 artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real S. cerevisiae datasets. In the 2-dataset case, we show that MDI’s performance is comparable to the present state of the art. We then move beyond the capabilities of current approaches and integrate gene expression, ChIP-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques – as well as to non-integrative approaches – demonstrate that MDI is very competitive, while also providing information that would be difficult or impossible to extract using other methods

Salmon for Terrestrial Protected areas

Although managers safeguard protected areas for migratory species, little consideration has been given to how migratory species might benefit parks. Additionally, whereas land‐sea connections are considered in management of protected areas, most effort has focused on reducing negative “downstream” processes. Here, we offer a proposal to promote positive “upstream” processes by safeguarding the seasonal pulse of marine nutrients imported into freshwater and riparian ecosystems by spawning migrations of Pacific salmon. Currently, high rates of fishing limit this important contribution to species and processes that terrestrial parks were designed to protect. Accordingly, we propose limiting exploitation in areas and periods through which salmon runs bound for terrestrial protected areas can migrate. Best suited for less commercially valuable but relatively abundant and widespread pink and chum salmon (O. gorbuscha and keta), our proposal thus considers ecosystem and societal needs for salmon. We conclude by outlining strategies to overcome socio‐economic barriers to implementation