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Yes / The major components of human diet both past and present may be estimated by measuring the carbon and nitrogen isotope ratios (δ13C and δ15N) of the collagenous proteins in bone and tooth dentine. However, the results from these two tissues differ substantially: bone collagen records a multi-year average whilst primary dentine records and retains timebound isotope ratios deriving from the period of tooth development. Recent studies harnessing a sub-annual temporal sampling resolution have shed new light on the individual dietary histories of our ancestors by identifying unexpected radical short-term dietary changes, the duration of breastfeeding and migration where dietary change occurs, and by raising questions regarding factors other than diet that may impact on δ13C and δ15N values. Here we show that the dentine δ13C and δ15N profiles of workhouse inmates dating from the Great Irish Famine of the 19th century not only record the expected dietary change from C3 potatoes to C4 maize, but when used together they also document prolonged nutritional and other physiological stress resulting from insufficient sustenance. In the adults, the influence of the maize-based diet is seen in the δ13C difference between dentine (formed in childhood) and rib (representing an average from the last few years of life). The demonstrated effects of stress on the δ13C and δ15N values will have an impact on the interpretations of diet in past populations even in slow-turnover tissues such as compact bone. This technique also has applicability in the investigation of modern children subject to nutritional distress where hair and nails are unavailable or do not record an adequate period of time. / This study was supported by an Arts and Humanities Research Council grant funding to JB under AHRC Studentship AH/I503307/1.

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Streptococcus mutans is a facultative member of the oral plaque and is associated with dental caries. It is able to survive long periods of sugar starvation. The purpose of this project was to explore specific avenues that S. mutans may use in order to cope with carbohydrate deprivation. Intracellular polysaccharide (IPS) is accumulated by S. mutans when grown in excess sugar, and can contribute towards the cariogenicity of S. mutans. Inactivation of the glgA gene, encoding a putative glycogen synthase, prevented accumulation of IPS in batch cultures grown with excess glucose or sucrose. Inactivation of the pul gene, encoding a putative pullulanase which is thought to be involved in IPS catabolism, did not prevent IPS accumulation. IPS was found to be important for the persistence of S. mutans grown in batch culture with excess glucose, and then starved of glucose. In these conditions, the IPS was largely used up within one day of starvation, and yet survival of the parental strain was extended by at least 15 days beyond that of the glgA and pul mutants; potentially, some feature of IPS metabolism, distinct from providing nutrients, is important for persistence. IPS was not needed for persistence when sucrose was carbon source or when mucin was present in batch cultures. IPS accumulation was not clearly demonstrated in biofilm conditions. When grown in condition permissive for IPS accumulation, biofilms of the glgA and pul mutants did not show decreased survival, compared to the parental strain. It is plausible that, within a biofilm, S. mutans can use alternative sources of energy (like the extracellular matrix) to compensate for the lack of IPS. To look at specific genes upregulated by sugar starvation, microarrays analysis was performed on S. mutans batch cultures. Some of the genes upregulated by starved, stationary phase bacteria, appeared to be organized in an operon, thought to encode components of the pyruvate dehydrogenase (PDH) complex. Northern Blot analysis showed that pdhD and the downstream genes, pdhA, pdhB and pdhC, form an operon that is transcribed predominantly in stationary phase. Inactivation of pdhD impaired survival of both batch cultures and biofilms. Analysis with fluorescent reporters revealed a distinct expression pattern for the pdh promoter, with less than 1% of stationary phase bacteria displaying pdh expression. When first detected, after one day of sugar starvation, expression was in individual bacteria. At later times, expressing bacteria were often in chains. The lengths of chains increased with time suggesting growth and division. It is likely that the pdh-expressing sub-population is able to persist for extend times in stationary phase. / Microbiology and Immunology

Phosphate (Pi) is an essential nutrient for plants, required for plant growth and seed viability. When Pi is limited, plants undergo dynamic morphological and metabolic changes to leverage available Pi, known as the Phosphate Starvation Response (PSR). The inositol phosphate (InsP) signaling pathway is a crucial element of the plant's ability to regulate the PSR and respond to changing energy conditions. InsPs are synthesized from the cyclic 6-carbon polyol scaffold, myo-inositol. Inositol hexakisphosphate (InsP6) is the most abundant InsP signaling molecule and can be phosphorylated by the multifunctional inositol tetrakisphosphate 1-kinase 1 (ITPK1) and diphosphoinositol pentakisphosphate (VIP) kinases, resulting in inositol pyrophosphates (PP-InsPs). PP-InsPs have high energy bonds and have been linked to Pi maintenance and energy homeostasis in yeast, plants, and mammals. However, the precise mechanism(s) by which PP-InsPs act within plant signaling pathways remains to be determined. Two approaches to understand the role of PP-InsPs in plants are described within this dissertation. The first approach analyzes genetic loss-of-function vip1/vip2 double mutants, and their responses to low Pi conditions. Specifically, vip1/vip2 double mutant gene expression and lipid remodeling patterns in response to low Pi were characterized. We found that vip1-2/vip2-2 had an impacted lipid remodeling response under low Pi conditions, whereas ipk1 had altered lipid composition under Pi-replete conditions. In a complementary approach, a gain-of-function in either the ITPK1 or the kinase domain of VIP (VIP2KD) were constructed in transgenic Arabidopsis thaliana plants. Both ITPK1 and VIP2KD transgenic plants contain elevated levels of the specific inositol pyrophosphate, InsP8. Elevated InsP8 in both types of plants results in changes in growth and senescence phenotypes, delayed time to flowering, Pi accumulation, and altered PSR gene expression. The data from both approaches suggest new roles for PP-InsPs in the regulation of the PSR and other signaling pathways in plants. To enhance my teaching and leadership skills, I participated in the Graduate Teaching Scholars (GTS) program. As a GTS, I worked with the Virginia Tech Research and Extension Experiential Learning (VT-REEL) program where I developed a structured mentorship program for undergraduate and graduate students and created a professional development workshop series. During the COVID-19 pandemic, I developed an online version of the VT-REEL program. Using inclusive pedagogy practices and surveys from the participants, we compiled the best practices for moving a summer undergraduate research program online. These practices come from surveyed participants in the 2020 and provides strategies that can be tailored to various online research experiences and be implemented in both online and in-person formats. / Doctor of Philosophy / Phosphate (Pi) is crucial for plant development and crop yield, but is often limited in soils. Pi-containing fertilizers are often added to supplement soils. Overuse of Pi-containing fertilizers can lead to Pi runoff and can devastate aquatic ecosystems. In addition, Pi is a limited, nonrenewable resource, with U.S. stores projected to be depleted in as little as 30 years. It is now crucial to develop crops that can feed a growing population with less Pi input. Here, we describe how changing levels of plant messenger molecules known as inositol pyrophosphates (PP-InsPs) impact the ability of plants to sense and respond to Pi. This knowledge advances understanding f how mineral nutrient physiology affects many plants traits, and can be harnessed to develop novel strategies to reduce Pi-application and overuse.

In cells and organelles transporters are responsible for translocation of amino acids, sugars and nucleotides among others. In the central nervous system (CNS), amino acid transporters can function as neurotransmitter transporters and nutrient sensors. The Solute carrier (SLC) superfamily is the largest family of transporters with 395 members divided in 52 families. The system A and system N amino acid transporter family, SLC38, consists of 11 members, SNAT1-11 (SLC38A1-11). The members are expressed in the brain, exclusively in neurons or astrocytes and some in both. Amino acid signaling is mainly regulated via two pathways, the amino acid responsive (AAR) pathway and the mechanistic/mammalian target of rapamycin complex 1 (mTORC1) pathway. These pathways regulate the protein synthesis in opposite directions depending on the amino acid availability. SLC38 members along with other SLCs have been identified to participate in these pathways. In paper I, the regulation of SLC genes after complete amino acid starvation in mouse hypothalamic cells have been studied with microarray and we found that 47 SLC genes were significantly altered at five hours of starvation. Interestingly, we found that Slc38a1 and Slc38a7 were upregulated along with the known starvation responding gene, Slc38a2. A complementary starvation study for the SLC38 genes was performed using primary mouse embryonic cortex cells. We found that Slc38a1, Slc38a2, Slc38a5, Slc38a6 and Slc38a8 were upregulated while Slc38a3, Slc38a7 and Slc38a11 were downregulated. Three members from the SLC38 family, SNAT8 (paper IV), SNAT9 (paper III) and SNAT10 (paper II) have been histologically characterized in mouse brain and all these transporters are exclusively neuronal. SNAT8 and SNAT10 were also functionally characterized and shown to be transporters for alanine and glutamine among others. SNAT8 was shown to mediate sodium dependent transport and was classified to system A. SNAT10 was shown to be a sodium independent bidirectional transporter and displayed characteristics for system A and N. SNAT9 is a lysosomal component of the Ragulator-Rag complex which senses amino acid availability and activates mTORC1. In paper III we also found that Slc38a9 gene expression was upregulated following starvation and downregulated following high-fat diet in mouse brain.