About

Shuo Han is an Assistant Professor of Biochemistry and an Assistant Professor in Molecular Genetics and Microbiology at Duke University. He is a member of the primary faculty in the Department of Biochemistry. His research focuses on biochemistry and molecular genetics, contributing to the understanding of fundamental biological processes. Further details about his specific research interests, background, and key contributions are not provided on the page.

Research topics

• Internal medicine
• Biology
• Medicine
• Biochemistry
• Endocrinology
• Genetics
• Virology

Selected publications

• ARGOS Genes in Cauliflower: Genome-Wide Identification and Functional Validation of BobARL2 Under Abiotic Stresses

  International Journal of Molecular Sciences · 2025-10-09

  articleOpen access

  The Auxin-Regulated Gene Involved in Organ Size (ARGOS) proteins have crucial regulatory effects on organ size and responses to environmental stresses. Despite their importance, Brassica oleracea ARGOS gene members and their functions in response to abiotic stresses have not been thoroughly investigated. In this study, we identified 40 ARGOS genes via a genome wide analysis of cauliflower and two other B. oleracea morphotypes as well as Brassica rapa, Brassica nigra, and Raphanus sativus. Expression pattern analyses indicated that these genes are responsive to multiple abiotic stresses, including salinity, heat, cold, and diverse hormones. Notably, the expression of an ARGOS-like gene (BobARL2) was upregulated in cauliflower treated with 1-aminocyclopropane-1-carboxylic acid (ACC). Moreover, the overexpression of BobARL2 decreased ethylene sensitivity, resulting in less inhibition of root elongation compared to the wild-type. Additionally, the overexpression lines exhibited enhanced salt tolerance. A yeast two-hybrid assay and luciferase complementation imaging (LCI) assay confirmed that BobARL2 can interact with Reversion-to-ethylene sensitivity Like4 (BobRTL4), which negatively regulates ethylene signal transduction. These findings advance our understanding of the evolution and functional roles of ARGOS genes in cauliflower and other Brassicaceae species, particularly in relation to abiotic stress responses, while also offering valuable insights relevant to the genetic improvement and breeding of novel varieties.

  PublisherOA PDFDOI

• Human gut Bifidobacteria strains regulate host longevity via shared and divergent mechanisms in <i>C. elegans</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-17

  preprintOpen accessSenior authorCorresponding

  Abstract The human gut microbiome influences many aspects of host aging physiology. However, it is not clear how distinct bacterial strains interact with host aging pathways and different healthspan metrics. To investigate this question, we chose Bifidobacteria as our bacterial model. The Bifidobacteria genus contains diverse species that are enriched in both human infants and centenarians, suggesting that they may confer “youthful” effects in aging adults. We selected eleven strains from nine Bifidobacteria species that are commonly detected in human fecal samples. Using our human anaerobic gut bacteria– C. elegans aging platform, we examined 1) individual Bifidobacteria strains’ contribution to lifespan and healthspan and 2) their genetic interactions with the conserved, longevity-associated transcriptional regulators. We identified two B. longum and B. infantis strains that most strongly increased lifespan and stress resistance. Notably, these two strains act through shared (e.g., ATFS-1/ATF5, HSF-1/HFS1, and SKN-1/NRF2) and yet strain-specific pathways (e.g., NHR-49/PPARα for B. infantis ) to enhance both lifespan and oxidative stress protection. Lastly, both strains activate a panel of genes involved in molecular chaperone, antioxidant, and lipid remodeling activities, serving as candidate cytoprotective mechanisms for further investigations. In summary, this study establishes a framework of dissecting the mechanistic links between human anaerobic gut bacteria and conserved host aging pathways that can be applicable beyond Bifidobacteria. While the connections between gut microbiome and aging in humans are complex, our approach provides the beginning steps to uncover strain-level interactions that may ultimately inform targeted probiotic strategies for promoting healthy aging.

  PublisherOA PDFDOI

• Significance of glutathione in the hormesis effect: a case study of the relationship between heavy metal Cd and monitoring plant Tillandsia ionantha

  Plant Physiology and Biochemistry · 2025-06-02 · 4 citations

  article
  PublisherDOI

• Trade-offs of different types of dose-responses following temporal gradients of Pb stress in <i>Tillandsia usneoides</i>

  Environmental Toxicology and Chemistry · 2025-01-22 · 1 citations

  article

  The dose-response relationship between toxicants and organisms is the most fundamental principle in toxicological risk assessment. However, multiphasic nonlinear responses are poorly understood, and the underlying mechanisms remain elusive. In this study, we subjected the indicator plant Tillandsia usneoides to 5 or 10 time gradients of 1 mM Pb and assessed the response patterns of five damage markers and eight resistance markers in the leaves. The results showed that in the assay with five time gradients, 10 out of 13 biomarkers showed biphasic responses and two biomarkers showed multiphasic responses. In the assay with 10 time gradients, six biomarkers showed biphasic responses and five biomarkers showed multiphasic responses. The results confirmed that increasing the number of dose gradients facilitates the detection of multiphasic dose responses. Additionally, the occurrence of nonlinear responses was found to be a common phenomenon. Further analysis of the frequency of trade-offs showed that the occurrence frequency of trade-off 2 (toxicants do not affect one marker but stimulate other markers) was always higher than that of trade-off 1 (toxicants worsen one marker while stimulating other markers) for both damage and resistance markers, and that trade-off 2 was more likely to appear in resistance markers. This suggests that as the duration of stress increases, the body produces more resistance substances, which coordinate with one another to maintain internal balance. This study suggests that the trade-off theory can be effectively used to elucidate the complex relationship between a toxicant and T. usneoides.

  PublisherDOI

• Root degradation of the epiphytic plant Tillandsia ionantha and its exclusion against four heavy metals

  Pakistan Journal of Botany · 2025-10-24

  article
  PublisherDOI

• Intradural calcifying pseudoneoplasm of the neuraxis in the lumbosacral canal: Two case reports and review of the literature

  International Journal of Surgery Case Reports · 2025-09-23

  articleOpen access1st author

  Calcifying pseudoneoplasms of the neuraxis (CAPNON) are benign and slowly growing fibro-osseous lesions of the nervous system. We report two rare cases of spinal CAPNON and provide a literature review. A 33-year-old woman with back pain underwent lumbar magnetic resonance imaging (MRI), revealing a large intradural mass (1.5 × 0.9 × 10.6cm 3 ) at L2-S1. Postoperative MRI scan performed 3 years after surgery confirmed no recurrence. A 64-year-old woman with lower limb numbness and gait instability underwent lumbar MRI, revealing an L3 intradural mass (1.1 × 0.3 × 1.6cm 3 ). Lower limb numbness were resolved after surgery during 1 year follow-up. Accurate recognition of CAPNON is essential to guide appropriate surgical intervention due to its favorable prognosis. In these situations, complete resection and radiological follow-up are highly recommended. • The first case of 10.6 cm intradural CAPNON in the lumbosacral canal spanning five spinal segments and we review the literature briefly. • Current recommendations for the management of spinal CAPNON are discussed. • Differentiation of spinal CAPNON from true tumors is critical to avoid unnecessary treatments due to its favorable prognosis.

  PublisherDOI

• Metabolomic Applications in Gut Microbiota-Host Interactions in Human Diseases

  Gastroenterology Clinics of North America · 2024-01-23 · 2 citations

  reviewSenior authorCorresponding
  PublisherDOI

• A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

  Plant Communications · 2024-01-01 · 34 citations

  articleOpen access

  The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

  PublisherDOI

• DECIPHERING THE CHEMICAL LANGUAGE OF GUT BACTERIA IN AGING AND LONGEVITY

  Innovation in Aging · 2024-12-01

  articleOpen access1st authorCorresponding

  Abstract The human gut microbiota encodes diverse metabolic pathways, where gut microbes make numerous compounds that are relevant to human health and hold untapped therapeutic potential. Fecal microbiota transplantation has been shown to delay age-associated decline in mouse and fish models. However, how specific gut bacteria and their metabolites impact host physiology represent a new frontier that remains to be fully explored. Leveraging our expertise in the gut microbiome and aging biology, we tackle this underexplored area from both the microbial and host’s perspectives. Specifically, our lab seeks to 1) mechanistically characterize gut bacteria and bioactive small molecules in host aging and physiology, and 2) identify gut microbial-dependent, host cellular mechanisms underlying organismal health-span and lifespan. We aim to understand how gut bacteria mechanistically contribute to host aging and longevity and to identify new molecular targets to delay age-associated decline.

  PublisherDOI

• High-throughput identification of gut microbiome-dependent metabolites

  Nature Protocols · 2024-05-13 · 15 citations

  review1st authorCorresponding
  PublisherDOI

Frequent coauthors

• Dwight D. Koeberl

  Duke Medical Center

  29 shared

• Sudha K. Shenoy

  Duke University Health System

  18 shared

• Songtao Li

  Zhejiang Chinese Medical University

  18 shared

• Neil J. Freedman

  Duke Medical Center

  12 shared

• Jiao‐Hui Wu

  Duke Medical Center

  10 shared

• Priya S. Kishnani

  Duke Medical Center

  9 shared

• Kunhong Xiao

  Allegheny Health Network

  9 shared

• James W. Wisler

  Duke Medical Center

  9 shared

Labs

• The Han LabPI

Education

• Postdoctoral Fellow, Laboratory of Justin Sonnenburg, Microbiology & Immunology

  Stanford University School of Medicine

  2022

• Ph.D., Laboratory of Anne Brunet, Genetics

  Stanford University School of Medicine

  2017

• B.S., Biology

  Massachusetts Institute of Technology

  2009