Thomas Smith

Dr. Thomas Smith

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Research Focus & Metrics

Academic Career Length

22Years (2005-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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21 January 2020 in Proceedings of the National Academy of Sciences
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TSThomas Smith
Thomas Smith
NMNancy A. Moran
Nancy A. Moran
Symbioses between animals and microbes are often described as mutualistic, but are subject to tradeoffs that may manifest as shifts in host and symbiont metabolism, cellular processes, or symbiont density. In pea aphids, the bacterial symbiont Buchnera is confined to specialized aphid cells called bacteriocytes, where it produces essential amino acids needed by hosts. This relationship is dynamic; Buchnera titer varies within individual aphids and among different clonal aphid lineages, and is affected by environmental and host genetic factors. We examined how host genotypic variation relates to host and symbiont function among seven aphid clones differing in Buchnera titer. We found that bacteriocyte gene expression varies among individual aphids and among aphid clones, and that Buchnera gene expression changes in response. By comparing hosts with low and high Buchnera titer, we found that aphids and Buchnera oppositely regulate genes underlying amino acid biosynthesis and cell growth. In high-titer hosts, both bacteriocytes and symbionts show elevated expression of genes underlying energy metabolism. Several eukaryotic cell signaling pathways are differentially expressed in bacteriocytes of low- versus high-titer hosts: Cell-growth pathways are up-regulated in low-titer genotypes, while membrane trafficking, lysosomal processes, and mechanistic target of rapamycin (mTOR) and cytokine pathways are up-regulated in high-titer genotypes. Specific Buchnera functions are up-regulated within different bacteriocyte environments, with genes underlying flagellar body secretion and flagellar assembly overexpressed in low- and high-titer hosts, respectively. Overall, our results reveal allowances and demands made by both host and symbiont engaged in a metabolic “tug-of-war.”

28 September 2007 in Ergonomics
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TSThomas Smith
Thomas Smith
The application of ergonomics/human factors (E/HF) principles and practices, and the implementation of ergonomics programmes, have achieved proven success in improving performance, productivity, competitiveness, and safety and health in most occupational sectors. However, the benefits that the application of E/HF science might bring to promoting student learning have yet to be widely recognized. This paper deals with the fundamental purpose of education – student learning – and with the question of how the ergonomic design of the learning environment influences learning performance. The underlying premise, embodied in the quote below, is that student learning performance to a substantial degree is context specific – influenced and specialized in relation to specific design factors in the learning environment. The basic scientific question confronting learning ergonomics is which design characteristics in the learning environment have the greatest influence on variability in learning performance. Practically, the basic challenge is to apply this scientific understanding to ergonomic interventions directed at design improvements of learning environments to benefit learning. This paper expands upon these themes by addressing the origins and scope of learning ergonomics, differing perspectives on the nature of learning, evidence for context specificity in learning and conclusions and research implications regarding an ergonomics perspective on learning.

1 January 2009 in WORK: A Journal of Prevention, Assessment & Rehabilitation
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Journal Article
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TSThomas Smith
Thomas Smith
KSKathleen Schoenbeck
Kathleen Schoenbeck
SCSandra Clayton
Sandra Clayton
This study collected staff responses to an occupancy quality survey before, and 6 and 22 months after, St. Paul Children's Hospitals and Clinics (CHC) replaced an open bay (OB) with a private room (PR) neonatal intensive care unit (NICU) design. Staff interview responses and task activity observations also were collected. The goal was to assess how this change would influence staff perceptions and performance. As a result of the transition from the OB to the PR environment: (1) rankings of overall physical environment, patient care, job, technology, and off-the-job quality significantly improved; but (2) rankings of patient care team interaction quality significantly declined. Results for the 22-month PR survey indicate essentially no meaningful changes in rankings of occupancy quality from the 6-month survey, suggesting no consolidation of quality gains in the intervening 16-month period. Written comments pertaining to private room NICU design issues by survey respondents, targeting problems with unit operations, may explain this finding. Collectively, the findings suggest that NICU operational management was not effectively modified to deal with the new design, and that an OB to PR NICU transition requires a systems approach to macroergonomic challenges imposed by the new design.

6 May 2022 in PLOS Genetics
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Journal Article
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TSThomas Smith
Thomas Smith
YLYiyuan Li
Yiyuan Li
JPJulie Perreau
Julie Perreau
NMNancy A. Moran
Nancy A. Moran
Pea aphids (Acyrthosiphon pisum) are insects containing genes of bacterial origin with putative functions in peptidoglycan (PGN) metabolism. Of these,rlpA1-5,amiD, andldcAare highly expressed in bacteriocytes, specialized aphid cells that harbor the obligate bacterial symbiontBuchnera aphidicola, required for amino acid supplementation of the host’s nutrient-poor diet. Despite genome reduction associated with endosymbiosis, pea aphidBuchneraretains genes for the synthesis of PGN whileBuchneraof many other aphid species partially or completely lack these genes. To explore the evolution of aphid horizontally-transferred genes (HTGs) and to elucidate how host and symbiont genes contribute to PGN production, we sequenced genomes from four deeply branching lineages, such that paired aphid andBuchneragenomes are now available for 17 species representing eight subfamilies. We identified all host and symbiont genes putatively involved in PGN metabolism. Phylogenetic analyses indicate that each HTG family was present in the aphid shared ancestor, but that each underwent a unique pattern of gene loss or duplication in descendant lineages. While four aphidrlpAgene subfamilies show no relation to symbiont PGN gene repertoire, the loss of aphidamiDandldcAHTGs coincides with the loss of symbiont PGN metabolism genes. In particular, the coincident loss of hostamiDand symbiontmurCEFin tribe Aphidini, in contrast to tribe Macrosiphini, suggests either 1) functional linkage between these host and symbiont genes, or 2) Aphidini has lost functional PGN synthesis and other retained PGN pathway genes are non-functional. To test these hypotheses experimentally, we used cell-wall labeling methods involving ad-alanine probe and found that both Macrosiphini and Aphidini retainBuchneraPGN synthesis. Our results imply that compensatory adaptations can preserve PGN synthesis despite the loss of some genes considered essential for this pathway, highlighting the importance of the cell wall in these symbioses.

1 January 2013 in WORK: A Journal of Prevention, Assessment & Rehabilitation
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TSThomas Smith
Thomas Smith
OBJECTIVE: This report introduces evidence for the conclusion that a common theme underlies almost all proposed solutions for improving the performance of K-12 students, namely their reliance on the design of educational system environments, features and operations. METHODS AND RESULTS: Two categories of design factors impacting such performance are addressed: (1) 9 factors reliably shown to have a strong influence – namely environmental design of classroom and building facilities, longer exposure to learning, cooperative learning designs, early childhood education, teaching quality, nutritional adequacy, participation in physical activity, good physical fitness, and school-community integration; and (2) 11 factors with an equivocal, varied or weak influence – classroom technology, online learning environments, smaller class size, school choice, school funding, school size, school start times, teacher training level, amount of homework, student self-confidence and informal learning. CONCLUSIONS: It is concluded that: (1) student learning outcomes, and more broadly the edifice of education itself, are largely defined in terms of an extensive system of design factors and conditions; (2) the time is long overdue for the educational system to acknowledge the central role of E/HF design as the major influence on student performance and learning; and (3) K-12 educators and administrators should emphasize allocation of resources to design factors reliably shown to have a strongly positive impact on student performance, but should treat expenditure on factors with equivocal, varied or weak influence on such performance with more caution and/or skepticism.

21 December 2021 in mBio
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Journal Article
Open access
TSThomas Smith
Thomas Smith
MLMijoon Lee
Mijoon Lee
MPMaria D. Person
Maria D. Person
DHDusan Hesek
Dusan Hesek
SMShahriar Mobashery
Shahriar Mobashery
NMNancy A. Moran
Nancy A. Moran
Most enzymes are capable of performing biologically irrelevant side reactions. During evolution, promiscuous enzyme activities may acquire new biological roles, especially after horizontal gene transfer to new organisms.