Doctor of Philosophy

dissertationThe endoplasmic reticulum (ER) is a dynamic organelle that is responsible for the folding and quality control of proteins within the endomembrane system. Both physiological and pathological conditions can result in accumulation of misfolded proteins within the ER, a situation termed ER stress, which results in cell death if not alleviated. Perturbations in ER function result in activation of three ER transmembrane proteins (Ire1, Perk, and Atf6) that are primarily responsible for facilitating the unfolded protein response (UPR). Activation of the UPR initially increases ER capacity to offset the surge in misfolded protein; however, during irremediable stress, the UPR activates pro-apoptotic pathways presumably to prevent the cytotoxic consequences of secreting misfolded proteins. Ire1 is an endoribonuclease that is responsible for the unconventional splicing of an intron from the transcription factor, Xbp1. However, Ire1 is also responsible for the direct degradation of a number of mRNAs, a process termed regulated Ire1-dependent decay (RIDD). In mammals, long-term activation of Ire1 results in nonspecific cleavage of ER-localized mRNAs and subsequent cell death. However, at early time points a limited number of mRNAs are prioritized to the RIDD pathway and are degraded relatively rapidly. In the work presented here, I address the questions of (1) how specific mRNAs are prioritized for degradation? And (2) what is the function mRNA degradation during acute of ER stress? I have found that specific nucleotide sequence and structural motifs are used to target mRNAs to the RIDD pathway in both fly and mammalian cells. Furthermore, I show that inhibiting translation of these motifs is also essential for RIDD targeting. Lastly, I show Ire1-dependent effects on lysosome accumulation during ER stress; this may enhance prosurvival signaling of the UPR. These data provide insight into the mechanisms of Ire1 function as well as a model for how the RIDD pathway may function in both the prosurvival and pro-apoptotic pathways of the UPR

Adult-Child Sexual Contact: Examining Mental Health Trainees’ Perception of the Impact on Adult Psychological-Emotional Status

Thirty-eight graduate students enrolled in mental health-related programs completed the Brief Symptom Inventory (BSI) indicating anticipated impact of adult-child sexual contact on the psychological status of a young adult woman from positive family environment and one from a negative family environment. BSI subscale scores were significantly higher than the BSI general population’s mean scores in both cases. Multiple regression analyses found that: in the healthy family scenario, practitioners’ background variables (parent education, family of origin climate, prior childhood sexual contact with an adult, and education) did not contribute significantly to the variance in their prediction of expectation of client’s overall psychological distress; and, in the dysfunctional family case, practitioners’ background (childhood experience with adult sexual contact, education level, and professional experience) contributed to 40% of the variance in their prediction of the client’s emotional state. Results of qualitative analyses are presented, and implications for training and service delivery discussed

Treatment and Management of Depression Symptoms in Pregnant Veterans: Varying Experiences of Mental Health Care in the Prenatal Period

Depression screening is recommended for all pregnant veterans; however, little is known on how often symptomatic women receive care, how depression treatment presents in practice, and whether women veterans are utilizing treatment during the appreciable perinatal period. Our sample included 142 pregnant veterans from 15 Veterans Health Administration (VA) medical facilities with Edinburgh Postnatal Depression Scale (EPDS) scores \u3e/=10. Sociodemographic characteristics, military service, health utilization, and pregnancy related factors were collected as part of a telephone survey. A majority of our sample (70%) had 1 or more mental health visits or antidepressant prescriptions during pregnancy. Women with a history of depression had more mental health visits and a higher percentage of antidepressant use before and during pregnancy than women without a history of depression. Pregnant women veterans without a history of depression may be less likely to receive care for depression during pregnancy. However, the majority of our veterans showing depression symptoms prenatally had at least one mental health visit or an antidepressant medication fill during their pregnancy window, suggesting that mental health care is readily available for women veterans

Evaluating RNAlater® as a preservative for using near-infrared spectroscopy to predict Anopheles gambiae age and species.

Mosquito age and species identification is a crucial determinant of the efficacy of vector control programmes. Near-infrared spectroscopy (NIRS) has previously been applied successfully to rapidly, non-destructively, and simultaneously determine the age and species of freshly anesthetized African malaria vectors from the Anopheles gambiae s.l. species complex: An. gambiae s. s. and Anopheles arabiensis. However, this has only been achieved on freshly-collected specimens and future applications will require samples to be preserved between field collections and scanning by NIRS. In this study, a sample preservation method (RNAlater(®)) was evaluated for mosquito age and species identification by NIRS against scans of fresh samples. Two strains of An. gambiae s.s. (CDC and G3) and two strains of An. arabiensis (Dongola, KGB) were reared in the laboratory while the third strain of An. arabiensis (Ifakara) was reared in a semi-field system. All mosquitoes were scanned when fresh and rescanned after preservation in RNAlater(®) for several weeks. Age and species identification was determined using a cross-validation. The mean accuracy obtained for predicting the age of young (<7 days) or old (≥ 7 days) of all fresh (n = 633) and all preserved (n = 691) mosquito samples using the cross-validation technique was 83% and 90%, respectively. For species identification, accuracies were 82% for fresh against 80% for RNAlater(®) preserved. For both analyses, preserving mosquitoes in RNAlater(®) was associated with a highly significant reduction in the likelihood of a misclassification of mosquitoes as young or old using NIRS. Important to note is that the costs for preserving mosquito specimens with RNAlater(®) ranges from 3-13 cents per insect depending on the size of the tube used and the number of specimens pooled in one tube. RNAlater(®) can be used to preserve mosquitoes for subsequent scanning and analysis by NIRS to determine their age and species with minimal costs and with accuracy similar to that achieved from fresh insects. Cold storage availability allows samples to be stored longer than a week after field collection. Further study to develop robust calibrations applicable to other strains from diverse ecological settings is recommended

Magnetism and magnetocaloric properties of Co1−x_{1-x}Mnx_xCr2_2O4_4

Co$_{1-x}$Mn$_x$Cr$_2$O$_4$ crystallizes as a normal spinel in the cubic $Fd \overline{3}m$ space group, and the end members have been reported to display a region of collinear ferrimagnetism as well as a low-temperature spin-spiral state with variable coherence lengths from 3 nm to 10 nm in polycrystalline samples. Here, we present the synthesis of the entire solid solution, and data showing that the ferrimagnetic ordering temperature as well as the spin-spiral lock-in temperature are tunable with the Co/Mn ratio. The peak magnetocaloric entropy change was determined to be $\Delta S_M$ = -5.63 J kg$^{-1}$ K$^{-1}$ in an applied magnetic field change of $\Delta H$ = 0 T to 5 T for the Mn end-member at the ferrimagnetic ordering temperature. Using density functional theory (DFT), we explore the shortcomings of the magnetic deformation proxy to identify trends in $\Delta S_M$ across composition in this spinel system, and explore future extensions of theory to address these discrepancies

High-throughput determination of Hubbard U and Hund J values for transition metal oxides via linear response formalism

DFT+U provides a convenient, cost-effective correction for the self-interaction error (SIE) that arises when describing correlated electronic states using conventional approximate density functional theory (DFT). The success of a DFT+U(+J) calculation hinges on the accurate determination of its Hubbard U and Hund's J parameters, and the linear response (LR) methodology has proven to be computationally effective and accurate for calculating these parameters. This study provides a high-throughput computational analysis of the U and J values for transition metal d-electron states in a representative set of over 2000 magnetic transition metal oxides (TMOs), providing a frame of reference for researchers who use DFT+U to study transition metal oxides. In order to perform this high-throughput study, an atomate workflow is developed for calculating U and J values automatically on massively parallel supercomputing architectures. To demonstrate an application of this workflow, the spin-canting magnetic structure and unit cell parameters of the multiferroic olivine LiNiPO4 are calculated using the computed Hubbard U and Hund J values for Ni-d and O-p states, and are compared with experiment. Both the Ni-d U and J corrections have a strong effect on the Ni-moment canting angle. Additionally, including a O-p U value results in a significantly improved agreement between the computed lattice parameters and experiment.Comment: 18 pages, 6 figure

A qualitative study examining the benefits and challenges of incorporating patient-reported outcome substance use and mental health questionnaires into clinical practice to improve outcomes on the HIV care continuum.

BACKGROUND: Inadequate identification and treatment of substance use (SU) and mental health (MH) disorders hinders retention in HIV care. The objective of this study was to elicit stakeholder input on integration of SU/MH screening using computer-assisted patient-reported outcomes (PROs) into clinical practice. METHODS: We conducted semi-structured interviews with HIV-positive patients who self-reported SU/MH symptoms on a computer-assisted PROs (n = 19) and HIV primary care providers (n = 11) recruited from an urban academic HIV clinic. Interviews were audio-recorded and transcribed. We iteratively developed codes and organized key themes using editing style analysis. RESULTS: Two themes emerged: (1) Honest Disclosure: Some providers felt PROs might improve SU/MH disclosure; more were concerned that patients would not respond honestly if their provider saw the results. Patients were also divided, stating PROs could help overcome stigma but that it could be harder to disclose SU/MH to a computer versus a live person. (2) Added Value in the Clinical Encounter: Most providers felt PROs would fill a practice gap. Patients had concerns regarding confidentiality but indicated PROs would help providers take better care of them. CONCLUSIONS: Both patients and providers indicated that PROs are potentially useful clinical tools to improve detection of SU/MH. However, patients and providers expressed conflicting viewpoints about disclosure of SU/MH using computerized PROs. Future studies implementing PROs screening interventions must assess concerns over confidentiality and honest disclosure of SU/MH to understand the effectiveness of PROs as a clinical tool. More research is also needed on patient-centered integration of the results of PROs in HIV care

Evaluating RNAlater® as a preservative for using near-infrared spectroscopy to predict Anopheles gambiae age and species.

BACKGROUND: Mosquito age and species identification is a crucial determinant of the efficacy of vector control programmes. Near-infrared spectroscopy (NIRS) has previously been applied successfully to rapidly, non-destructively, and simultaneously determine the age and species of freshly anesthetized African malaria vectors from the Anopheles gambiae s.l. species complex: An. gambiae s. s. and Anopheles arabiensis. However, this has only been achieved on freshly-collected specimens and future applications will require samples to be preserved between field collections and scanning by NIRS. In this study, a sample preservation method (RNAlater(®)) was evaluated for mosquito age and species identification by NIRS against scans of fresh samples. METHODS: Two strains of An. gambiae s.s. (CDC and G3) and two strains of An. arabiensis (Dongola, KGB) were reared in the laboratory while the third strain of An. arabiensis (Ifakara) was reared in a semi-field system. All mosquitoes were scanned when fresh and rescanned after preservation in RNAlater(®) for several weeks. Age and species identification was determined using a cross-validation. RESULTS: The mean accuracy obtained for predicting the age of young (<7 days) or old (≥ 7 days) of all fresh (n = 633) and all preserved (n = 691) mosquito samples using the cross-validation technique was 83% and 90%, respectively. For species identification, accuracies were 82% for fresh against 80% for RNAlater(®) preserved. For both analyses, preserving mosquitoes in RNAlater(®) was associated with a highly significant reduction in the likelihood of a misclassification of mosquitoes as young or old using NIRS. Important to note is that the costs for preserving mosquito specimens with RNAlater(®) ranges from 3-13 cents per insect depending on the size of the tube used and the number of specimens pooled in one tube. CONCLUSION: RNAlater(®) can be used to preserve mosquitoes for subsequent scanning and analysis by NIRS to determine their age and species with minimal costs and with accuracy similar to that achieved from fresh insects. Cold storage availability allows samples to be stored longer than a week after field collection. Further study to develop robust calibrations applicable to other strains from diverse ecological settings is recommended