About

Andrew James Jones, M.D., is an Associate Physician and Associate Program Director in the Department of Family and Community Medicine at UC Davis Medical Group. He is a general family medicine provider offering both preventative and treatment-focused care for patients of all ages, from infants and children to adults and geriatrics. His clinical interests include chronic disease management such as hypertension, diabetes, and substance use, as well as musculoskeletal injuries and reproductive counseling. Dr. Jones believes his role in healthcare is as a partner to his patients to help them reach their health goals through education, lifestyle changes, preventative health measures, and medication management. He aims to assist patients in making decisions about their health that enable them to live fulfilling lives for as long as possible.

Research topics

• Biology
• Biochemistry
• Genetics
• Food science
• Stereochemistry
• Chemistry
• Botany
• Ecology
• Neuroscience
• Bioinformatics

Selected publications

• Diversity of metabolomic findings regarding lung function in children and young adults

  American Journal of Respiratory and Critical Care Medicine · 2025-10-24

  article
  PublisherDOI

• Microbial community development and evolution in kinetic tests of sulfide-bearing rock over two years of operation

  Abstracts with programs - Geological Society of America · 2025-01-01

  articleSenior author
  PublisherDOI

• Cyanoglobule lipid droplets are a stress-responsive metabolic compartment of cyanobacteria and the progenitor of plant plastoglobules

  The Plant Cell · 2025-05-22 · 10 citations

  articleOpen access

  Lipid droplets (LDs) are well integrated into multiple facets of cellular physiology and potentially represent an effective platform for engineering heterologous metabolic pathways. LDs of chloroplasts, known as plastoglobules, mediate stress tolerance through dynamic and reversible changes to morphology and molecular composition. However, the dynamics and functional role(s) of cyanobacterial LDs are almost wholly unknown. Here, we have characterized the morphological behavior and quantitative proteome and lipidome of cyanobacterial LDs of Synechocystis sp. PCC 6803 grown under permissive or phosphorous-deficient media for 7 d. Our results show that cyanobacterial LDs are a metabolically active subcompartment of cyanobacteria with dynamic morphology and composition. The cyanobacterial LD proteome and lipidome are qualitatively similar to those of plant plastoglobules including an enrichment of prenyl lipids and the presence of twelve orthologs of Arabidopsis thaliana plastoglobule proteins. In view of these results, we propose that cyanobacterial LDs be named as cyanoglobules. In addition, we established that various plastoquinone derivatives containing hydroxyl and/or acyl groups on their solanesyl tail or quinone head accumulate in cyanoglobules. Deletion mutants of selected cyanoglobule proteins exhibit impairments in growth, pigmentation, and photosynthesis. Our results collectively support an evolutionary relationship between cyanoglobules and plastoglobules and reveal a possible central role for cyanoglobules in organismal physiology and stress adaptation.

  PublisherOA PDFDOI

• SIMPLIFIED IN VITRO MATURATION (IVM) OF OOCYTES FROM OVARIAN TISSUE (OT)

  Fertility and Sterility · 2025-12-01

  article
  PublisherDOI

• Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

  Science Advances · 2024-04-24 · 18 citations

  articleOpen access

  Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis, SlASAT1-LIKE ( SlASAT1-L ), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence that ASAT1-L arose through duplication of its paralog, ASAT1 , and was trichome-expressed before acquiring root-specific expression in the Solanum genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.

  PublisherOA PDFDOI

• The evolution of the disaster risk management cycle and its continuing applicability to an evolving flood threat

  Edward Elgar Publishing eBooks · 2024-04-16 · 2 citations

  book-chapter1st authorCorresponding

  Globally, hydroclimatic hazards are becoming more frequent and severe, driven by a warming climate and urbanization. With the evolving nature of flooding, research focus remains strong in this discipline. However, despite the changing nature of hydroclimatic hazards, the importance of the disaster management cycle has endured. Since its inception in 1979, the cycle has evolved, enabled by its open-system nature, through the inclusion of additional stages and stage weightings. Interpretation of the cycle has proven particularly influential in understanding how practitioners have focused most significantly on the mitigation and post-disaster stages substantiated by their continuing dominance in flood risk management. However, contemporary research and disaster risk reduction frameworks such as the Global Sendai Framework stress the importance of the preparedness stage in assisting society with an effective response and recovery. Therefore, increased research focus on the preparedness stage is viewed as a facilitator for an effective response and recovery.

  PublisherDOI

• Evaluating the impact of reciprocal teaching embedded within a Web 2.0 tool upon fifth-grade students’ reading during integrated readers’ workshop at a Professional Development School

  PDS Partners Bridging Research to Practice · 2024-12-16 · 1 citations

  articleOpen access1st author

  Purpose For this study, 12 fifth-grade students read expository text, employed reciprocal teaching strategies, collaborated face to face online using a Web 2.0 tool during the reading workshop. The purpose of this action research was to evaluate the impact of reciprocal teaching embedded in the Wakelet Curation Tool, a Web 2.0 tool, on fifth-grade students’ reading for comprehension, reading attitudes and perceptions of the innovation in an integrated reading class at an urban characteristic (Milner et al. , 2018) Professional Development School (PDS) (National Association for Professional Development Schools, 2021) site. Design/methodology/approach This action research followed a convergent parallel mixed-methods design. Two quantitative data collection instruments were used. Inferential and descriptive statistical tests were run to analyze quantitative data. Findings Findings showed the posttest scores for the Comprehension Content Knowledge test were not significantly higher than the pretest scores, but there was an increase from pre- to posttest. ERAS scores showed there was not an increase from pre- to postsurvey. In addition to quantitative data, qualitative data were collected and analyzed using inductive analysis. Four individual semi-structured interviews yielded the qualitative data for this study. Four themes were identified over the course of two coding cycles: (1) contributions of fifth-grade students’ perceptions about the innovation, (2) affective contributions, (3) reading achievement and (4) suggestions for future use. The data suggested participants acquired content-specific knowledge and strategies for monitoring and assessing their comprehension. Originality/value The information in this article explains the steps that the Outstanding Dissertation Award winner completed in order to apply for the PDS award. The article describes the action research that was conducted with fifth grade students to see how reciprocal teaching embedded within Wakelet Curation Tool impacted their reading comprehension.

  PublisherOA PDFDOI

• Trading acyls and swapping sugars: metabolic innovations in <i>Solanum</i> trichomes

  PLANT PHYSIOLOGY · 2024-05-15 · 11 citations

  articleOpen access

  Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by ACYLSUGAR ACYLTRANSFERASE (ASAT) enzymes from sugars and acyl-coenzyme A esters. Published research has revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars have been analyzed across a small fraction of the >1,200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the clade II species brinjal eggplant (Solanum melongena) led to the identification of eight unusual structures with inositol or inositol glycoside cores and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity, with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the brinjal eggplant ASAT 3-LIKE 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.

  PublisherOA PDFDOI

• Fucoxanthin levels in maternal serum at birth and eczema risk in offspring in early childhood: A birth cohort study

  Pediatric Allergy and Immunology · 2023-06-01 · 1 citations

  article

  Abstract Background Fucoxanthin, a marine xanthophyll carotenoid, has been shown to exert beneficial health effects. Cell‐based and animal‐based experimental studies have shown that fucoxanthin has the potential to mitigate eczema symptoms. Hence, we sought to assess whether fucoxanthinol 3‐arachidate, a fucoxanthin metabolite, measured in maternal serum at birth is associated with eczema development during early childhood. Methods Data from the 1989/1990 Isle of Wight birth cohort were analyzed. We focused on data obtained from the 1, 2, and 4 years follow‐ups. Fucoxanthinol 3‐arachidate was measured in maternal serum at the child's birth as abundance relative to the reference lipids. Eczema was ascertained according to parent‐reported clinical history and characteristic morphology and distribution. Log‐binomial regression models were used to estimate adjusted risk ratios (aRR) and their 95% confidence intervals (CI). Results A total of 592 subjects (49.2% males and 50.8% females) were included in the current analysis. Associations between fucoxanthinol 3‐arachidate levels and eczema risk during the first 4 years of life (longitudinal analysis) were evaluated using four modeling approaches, which showed higher fucoxanthinol 3‐arachidate levels were associated with reduced eczema risk: (i) aRR per 10 unit increase = 0.88, 95% CI: 0.76–1.03; (ii) aRR &gt;0 vs. =0 = 0.67, 0.45–0.99; (iii) aRR ≥2.3 vs. &lt;2.3 = 0.66, 0.44–0.98; and (iv) aRR tertile 3 vs. tertile 1 = 0.65, 0.42–0.99. Conclusion Our findings suggest that increased fucoxanthinol 3‐arachidate levels measured in maternal serum at the child's birth is associated with reduced eczema risk during the first 4 years of the offspring life.

  PublisherDOI

• Trading acyls and swapping sugars: metabolic innovations in <i>Solanum</i> trichomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-06-05 · 3 citations

  preprintOpen access

  Abstract Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by AcylSugar AcylTransferases from sugars and acyl-coenzyme A esters. Published research revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars were analyzed across a small fraction of the &gt;1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.

  PublisherOA PDFDOI

Recent grants

• MRI: Acquisition of Metabolite Profiling Mass Spectrometry Instrumentation for Michigan State University

  NSF · $467k · 2006–2009

Frequent coauthors

• Bruce D. Hammock

  University of California, Davis

  52 shared

• Venkatesh Balan

  University of Houston

  45 shared

• Robert L. Last

  Michigan State University

  44 shared

• Bruce E. Dale

  34 shared

• Shishir P. S. Chundawat

  Rutgers, The State University of New Jersey

  28 shared

• James R. Sanborn

  California Environmental Protection Agency

  22 shared

• Yoshiaki Nakagawa

  Kyoto University

  22 shared

• Ramin Vismeh

  Biotechnology Institute

  20 shared

Education

• Ph.D., Chemistry

  The Pennsylvania State University

  1983

• B. S., Chemistry

  Harvey Mudd College

  1976