Characterization of a Novel Sensing Mechanism Governing Antigenic Variation in P. Falciparum

Plasmodium falciparum expresses a multi-copy gene family called var in the intraerythroyctic stages of its life cycle in a mutually exclusive manner. var genes encode the chief antigenic and virulence determinant of P. falciparum, PfEMP1, and switching between active genes results in antigenic variation, allowing the parasite to evade the human immune system and cause chronic infections. The molecular mechanisms that control activation and silencing of individual var genes, as well as coordination of the switching process, presently remain incompletely defined. P. falciparum contains only ~60 var gene family members in its genome. Consequently, the question remains as to how this parasite can maintain an antigen-switch rate that allows for the emergence of a new variant when necessary, without rapidly exhausting all 60 members, to sustain chronic infections. The currently held paradigm proposes that antigenic variation follows an intrinsic, programed switching rate, operating independently of any external stimuli. In the following thesis I will present results suggesting the novel possibility that P. falciparum possesses cellular machinery capable of sensing changes in the environment of its host and is able to respond by altering antigen expression. It has been shown that changes in the transcription state of a var gene are controlled epigenetically. The methylation state of histone marks, deposited at active and silent var genes by histone methyltransferases (HMTs), play prominent roles in var gene regulation. Previously, Ukaegbu et al., 2015 showed that manipulating deposition of these marks had a striking impact on var gene expression. Metabolism and epigenetic control of gene expression are linked, as HMT activity is dependent on the intracellular concentrations of methyl donors, which can fluctuate based on nutrient availability. Various studies in other organisms have shown that there is a direct link between the level of intracellular S-adenosylmethionine (SAM), the principle methyl donor in biological methylation modifications, and histone methylation. I explored this connection between metabolism and var gene expression in P. falciparum. Parasites were cultured in growth media containing altered concentrations of nutrients involved in SAM metabolism. Bulk RNA was extracted from cultures, used as a template to synthesize cDNA, and analyzed by qPCR to determine the var gene expression at the population level. Conditions believed to increase SAM pools induced a coordinated switch to one particular var gene, var2csa, over time, phenocopying the results from Ukaegbu et al., 2015. This hypothesis was further tested by modifying expression of key enzymes involved in SAM metabolism. Once again, modifications thought to increase the intracellular level of SAM were found to induce a coordinated switch at the population level to var2csa. Conversely, modifications that lower the level of SAM did not induce expression of var2csa, but instead activated many vars at once across the population. These observations directly challenge the stochastic var switching paradigm by instead suggesting P. falciparum possesses the ability to sense environmental changes. After recognition of a pathogen, activated macrophages modify their microenvironments in various ways. I next tested the effect of two of these immune responses, depletion of amino acids and release of polyamines, on var expression of parasites in vitro. Both perturbations altered var expression, again specifically inducing var2csa. Taking these results together, I propose and discuss two possible models of antigenic variation in P. falciparum. The first centers on intracellular SAM metabolism in describing a promoter competition model governing var switching through var2csa. The second suggests that P. falciparum can sense when the host immune system first begins to recognize it via environmental cues resulting from antibody recognition, and respond by switching var gene expression. This would allow parasites to switch expression of var genes exactly when needed, allowing the most efficient utilization of their limited var gene repertoir

Using Sigma metrics to establish analytical product performance requirements and optimize analytical performance of an in vitro diagnostic assay using a theoretical total PSA assay as an example

Introduction: Establishing analytical performance requirements for in vitro diagnostic (IVD) assays is a challenging process. Manufacturers try to optimize analytical performance by choosing amongst many combinations of different product performance characteristics. Sigma metrics and method decision charts can be helpful aids in choosing appropriate analytical performance requirements. The objective of this research was to demonstrate the use of Sigma metrics and method decision charts to help establish analytical performance requirements and to optimize analytical performance at medical decision concentrations for an IVD assay. Materials and methods: A range of possible Sigma metrics were determined using three sources for total allowable error (TEa) and hypothetical total PSA assay results. Method decision charts were created for each TEa source and used to identify the maximum precision and bias that the assay could have to maintain sigma level performance of at least 3. Results: To achieve a sigma performance level of at least 3 for a hypothetical total PSA assay, the maximum allowable coefficient of variation ranged from 5.0% to 11.2% depending on the TEa source. To achieve a sigma performance level of at least 6, the maximum allowable coefficient of variation ranged from 2.5% to 5.6% depending on the TEa source. Conclusions: Using Sigma metrics and method decision charts when establishing analytical performance requirements can help manufacturers choose product requirements that will optimize IVD assay product performance

A Statistical Model for Risk Stratification on the Basis of Left Ventricular Ejection Fraction and Heart-Rate Turbulence

The MPIP data set was used to obtain a model for mortality risk stratification of acute myocardial infarction patients. The predictors heart rate turbulence (HRT) and left-ventricular ejection fraction (LVEF) were employed. HRT was a categorical variable of three levels; LVEF was continuous and its influence on the relative risk was explained by the natural logarithm function (found using fractional polynomials). Cox - PH model with HRT and lnLVEF was constructed and used for risk stratification. The model can be used to divide the patients into two or more groups according to mortality risk. It also describes the relationship between risk and predictors by a (continuous) function, which allows the calculation of individual mortality risk

HAZMAT VI: The Evolution of Extreme Ultraviolet Radiation Emitted from Early M Star

Quantifying the evolution of stellar extreme ultraviolet (EUV, 100 -- 1000 $\overset{\circ}{A}$) emission is critical for assessing the evolution of planetary atmospheres and the habitability of M dwarf systems. Previous studies from the HAbitable Zones and M dwarf Activity across Time (HAZMAT) program showed the far- and near-UV (FUV, NUV) emission from M stars at various stages of a stellar lifetime through photometric measurements from the Galaxy Evolution Explorer (GALEX). The results revealed increased levels of short-wavelength emission that remain elevated for hundreds of millions of years. The trend for EUV flux as a function of age could not be determined empirically because absorption by the interstellar medium prevents access to the EUV wavelengths for the vast majority of stars. In this paper, we model the evolution of EUV flux from early M stars to address this observational gap. We present synthetic spectra spanning EUV to infrared wavelengths of 0.4 $\pm$ 0.05 M$_{\odot}$ stars at five distinct ages between 10 and 5000 Myr, computed with the PHOENIX atmosphere code and guided by the GALEX photometry. We model a range of EUV fluxes spanning two orders of magnitude, consistent with the observed spread in X-ray, FUV, and NUV flux at each epoch. Our results show that the stellar EUV emission from young M stars is 100 times stronger than field age M stars, and decreases as t$^{-1}$ after remaining constant for a few hundred million years. This decline stems from changes in the chromospheric temperature structure, which steadily shifts outward with time. Our models reconstruct the full spectrally and temporally resolved history of an M star's UV radiation, including the unobservable EUV radiation, which drives planetary atmospheric escape, directly impacting a planet's potential for habitability.Comment: 23 pages, 15 figures, accepted to Ap

Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology

The Clinical Laboratory Improvement Amendments (CLIA) of 1988 requires that pharmacogenetic genotyping methods need to be established according to technical standards and laboratory practice guidelines before testing can be offered to patients. Testing methods for variants in ABCB1, CBR3, COMT, CYP3A7, C8ORF34, FCGR2A, FCGR3A, HAS3, NT5C2, NUDT15, SBF2, SEMA3C, SLC16A5, SLC28A3, SOD2, TLR4, and TPMT were validated in a CLIA-accredited laboratory. As no known reference materials were available, DNA samples that were from Coriell Cell Repositories (Camden, NJ) were used for the analytical validation studies. Pharmacogenetic testing methods developed here were shown to be accurate and 100% analytically sensitive and specific. Other CLIA-accredited laboratories interested in offering pharmacogenetic testing for these genetic variants, related to genotype-guided therapy for oncology, could use these publicly available samples as reference materials when developing and validating new genetic tests or refining current assays

Bringing arts interventions into care settings

Artistic and creative activities are increasingly recognised as tools to support people with dementia. They can share these activities on equal terms with everyone else and the arts can help them to overcome the barriers they often face through cultural participation and social engagement. Participation in artistic activities provides mental stimulation, exercises existing skills and offers new learning experiences

Resaca supports range expansion of invasive apple snails (Pomacea maculata Perry, 1810; Caenogastropoda: Ampullariidae) to the Rio Grande Valley, Texas

Resacas, or oxbow lakes, form from old river channels. In the Rio Grande, resacas provide habitat for diverse wildlife, including native and non-native species. Biologists unexpectedly found pink egg masses on emergent vegetation (November 2015) and later adult apple snails (May 2016) within a resaca at a former fish hatchery in Brownsville, Texas. This report extends the non-native range of Pomacea maculata Perry, 1810 by 429 km southeast in Texas. Our findings imply that abandoned waterbodies, such as fish hatcheries, can act as unrecognized conduits for non-native invasive species

Acceptance and commitment therapy for symptom interference in metastatic breast cancer patients: a pilot randomized trial

PURPOSE: Breast cancer is the leading cause of cancer mortality in women worldwide. With medical advances, metastatic breast cancer (MBC) patients often live for years with many symptoms that interfere with activities. However, there is a paucity of efficacious interventions to address symptom-related suffering and functional interference. Thus, this study examined the feasibility and preliminary efficacy of telephone-based acceptance and commitment therapy (ACT) for symptom interference with functioning in MBC patients. METHODS: Symptomatic MBC patients (N = 47) were randomly assigned to six telephone sessions of ACT or six telephone sessions of education/support. Patients completed measures of symptom interference and measures assessing the severity of pain, fatigue, sleep disturbance, depressive symptoms, and anxiety. RESULTS: The eligibility screening rate (64%) and high retention (83% at 8 weeks post-baseline) demonstrated feasibility. When examining within-group change, ACT participants showed decreases in symptom interference (i.e., fatigue interference and sleep-related impairment; Cohen's d range = - 0.23 to - 0.31) at 8 and 12 weeks post-baseline, whereas education/support participants showed minimal change in these outcomes (d range = - 0.03 to 0.07). Additionally, at 12 weeks post-baseline, ACT participants showed moderate decreases in fatigue and sleep disturbance (both ds = - 0.43), whereas education/support participants showed small decreases in these outcomes (ds = - 0.24 and - 0.18 for fatigue and sleep disturbance, respectively). Both the ACT and education/support groups showed reductions in depressive symptoms (ds = - 0.27 and - 0.28) at 12 weeks post-baseline. Group differences in all outcomes were not statistically significant. CONCLUSIONS: ACT shows feasibility and promise in improving fatigue and sleep-related outcomes in MBC patients and warrants further investigation