About

Jean-Yves Sgro is a distinguished senior scientist with extensive experience in using and teaching computer programs related to molecular graphics, computational methods, and data analysis. He has been at UW since 1986, holding a Ph.D. in Cellular and Molecular Biology from Université Joseph Fourier in Grenoble, France, and has researched at the European Molecular Biology Laboratory (EMBL). His work involves creating, organizing, and teaching workshops on molecular visualization, data analysis, and computational modeling, supporting the Department of Biochemistry and broader campus community. Sgro's research background includes 3D molecular visualization, RNA-folding predictions, sequence and data analysis, and the use of large computers for sequence analysis. His contributions include organizing hands-on tutorials and supporting biomolecular research through computational tools and visualization techniques.

Research topics

• Biochemistry
• Chemistry
• Botany
• Organic chemistry
• Biotechnology
• Chemical engineering
• Stereochemistry
• Biology

Selected publications

• Control strategies for high degree-of-freedom assistive devices using non-invasive body-machine interfaces: a survey and framework

  Disability and Rehabilitation Assistive Technology · 2026-03-16

  articleOpen access

  PURPOSE: Body-machine interfaces (BoMIs) provide individuals with movement impairments the ability to control assistive devices using signals from their body movements in a non-invasive and reliable way. However, high degree-of-freedom (DOF) assistive devices such as robotic manipulators require the user to control several device commands simultaneously and intuitively, which has resulted in limited adoption of these devices by the intended user population. In this review, we survey recent approaches for controlling high-DOF systems. MATERIALS AND METHODS: Based on a systematic literature search, we identified 25 articles that met our inclusion criteria. In each article, we specifically examined features of strategies related to two specific challenges: (i) simultaneously controlling a large number of DOFs, and (ii) making the interface more intuitive for the purpose of control. RESULTS: We found that (i) a majority of studies simplified the control problem by using only a few DOF at a time, and (ii) most interfaces were pre-defined with little or no customisation to the individual's movement abilities. We also found that most studies were still at a proof-of-concept stage focusing mainly on unimpaired participants, small sample sizes, and short training durations. CONCLUSION: Based on the results, we develop a high-level framework to classify these approaches that can serve as a basis for understanding current and future efforts in this domain. We also highlight factors that limit clinical relevance and translation and draw upon recent developments to provide recommendations for future research.

  PublisherDOI

• Upcycling Municipal Solid Waste to Polymers and Bioethanol

  Research Square · 2026-03-13

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Lateral Reactive Stepping Responses Differ Between Individuals with and without Transfemoral Amputation

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Genome of an <i>Escherichia coli</i> engineered for improved control over polyhydroxyalkanoate monomer composition

  Microbiology Resource Announcements · 2026-03-16

  articleOpen access

  LSBJ is a strain engineered to produce polyhydroxyalkanoate (PHA) from diverse carbon sources with enhanced control of PHA composition. We report a high-quality annotated genome with 98.68% completeness, 4,547 coding sequences, 75 tRNAs, and 1 copy each of the 5S, 16S, and 23S ribosomal RNA sequences.

  PublisherDOI

• Patterns of Microbial Succession and Niche Differentiation Across Depth and Age in a Landfill Have Implications for Management Strategies

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-01

  preprint

  Despite microorganisms being primarily responsible for landfill material decomposition, limited characterization has been performed across both landfill depth and age. Here, we investigated the microbial communities and physicochemical parameters in two active and two closed landfill wells from surface to bottom, as well as fill dirt and leachate at a sanitary landfill near Madison, Wisconsin, USA. Amplicon community sequencing fungi, bacteria and archaea revealed distinct microbial community structures across landfill sites. The observed patterns of microbial community succession by depth and age mirror the known phases of the landfill life cycle. Younger surface samples were dominated by aerobic fungi, which transitioned to fermentative bacteria and methanogenic archaea in older, deeper, layers. Simultaneously, high species richness was preserved across landfill ages, while reduced evenness at specific depths support spatial niche differentiation. In conjunction with the lack of trends found for physicochemical parameters by depth, this supports niche differentiation driven by the highly heterogenous waste inputs. This study provides the first comprehensive vertical profile of bacterial, fungal, and archaeal communities across landfill depths and ages, highlighting the influence of these parameters on physicochemical factors and microbial distribution within landfills. These results have implications for improving landfill management, including renewable gas energy production, minimizing emissions, and increasing degradation rates.

  PublisherDOI

• Lignin Removal in Subcellular Location of Poplar Cell Wall During Pretreatment Significantly Impacts Cellulose Digestibility

  ACS Sustainable Chemistry & Engineering · 2025-05-20 · 2 citations

  articleOpen access

  The γ-valerolactone (GVL) pretreatment is one of the leading solvent-based methods for producing high-quality lignin under mild conditions. However, the glucan conversion yield from GVL pretreated biomass remains unsatisfactory. To explore the discrepancies between the relatively low glucan conversion and high lignin extraction, we conducted GVL-HCl and NaOH pretreatments on poplar and investigated their effects on lignin content and location, as well as on enzymatic hydrolysis of poplar cell walls at the subcellular level. Under designated pretreatment conditions of GVL-HCl (90% GVL, 0.1 M HCl, 100 °C, 1 h) and NaOH (1 M, 121 °C, 2 h), the glucan conversion yields were 69.4% and 95.8%, with lignin removal rates of 67.8% and 47.7%, respectively. Four types of GFP-labeled carbohydrate binding modules were used to identify different forms of cellulose in the pretreated cell walls. The overall binding intensities to pretreated poplar were stronger for NaOH compared to GVL-HCl pretreatment. Stimulated Raman scattering microscopy imaging revealed that GVL-HCl preferentially extracted lignin from the compound middle lamella and cell corner areas, while NaOH effectively dissolved lignin in the secondary cell walls. Real-time imaging of cellulase degradation of pretreated cell walls further indicated that digestion started from both the cell lumen and the compound middle lamella areas for GVL, whereas it occurred uniformly across the secondary cell walls for NaOH. Our findings suggest that the location of lignin removal during pretreatment is crucial for enzymatic cellulose degradation, in addition to the total amount of lignin extraction.

  PublisherDOI

• Creation of an Acyltransferase Toolbox for Plant Biomass Engineering (Final Report)

  2025-04-02

  report1st authorCorresponding
  PublisherDOI

• <i>Populus</i> salicinoids: a thriving subfield in the omics era

  Tree Physiology · 2025-05-29 · 2 citations

  reviewOpen access

  Members of the salicaceous genus Populus are primarily used by plant biologists as a model system for understanding the genetic underpinnings of woody plant growth and development. Beyond their importance to those conducting developmental research, Populus spp. are key members of ecosystems in the Northern Hemisphere and show promise as a vital renewable source of biomass for sustainable biofuel production. This genus also produces a class of signature herbivore-deterring and medicinally significant phenolic glycosides, commonly referred to as salicinoids. Although salicinoids in Populus are primarily associated with defense against biotic disturbances, they have also been implicated in structuring the chemotaxonomy of Populus and Salicaceae, shaping endophytic microbiomes, directing abiotic stress responses and participating in primary metabolism. Despite advancements in understanding these interactions through functional genomics and biotechnological techniques such as CRISPR/Cas9, much about their function and biosynthesis still remains obfuscated. Here, we summarize a global view of progress made in Populus salicinoid research, focusing particularly on studies conducted through a biotechnological lens, to elucidate the distribution, ecological significance, and biosynthesis of these compounds.

  PublisherOA PDFDOI

• Multi-proteomics reveals integrated metabolic and regulatory networks for xylan catabolism in <i>Streptomyces</i> sp. SirexAA-E

  Microbiology Spectrum · 2025-11-20 · 1 citations

  articleOpen access

  ABSTRACT An insect-associated bacterium, Streptomyces sp. SirexAA-E (SirexAA-E) secretes plant biomass-degrading enzymes depending on the available cell wall materials. SirexAA-E readily utilizes xylan, one of the major hemicelluloses. However, the enzyme composition and pathways supporting xylan metabolism in SirexAA-E and other Streptomycetes have not been reported. We aimed to understand changes in both extracellular and intracellular protein productions by cultivating SirexAA-E in defined media containing either xylose, xylobiose, or xylan. Proteomics showed each carbon source gave specific extracellular protein composition when compared to glucose. Furthermore, intracellular proteomics using a pair-wise Tandem Mass Tag (TMT)-labeling LC-MS/MS identified 1,037 proteins with changes in the xylose-, xylobiose-, or xylan-dependent proteome relative to the glucose-derived proteome. We found that numerous proteins related to oxidative phosphorylation were enriched in the pentose-grown proteomes relative to the glucose proteome. This observation is consistent with a high demand for ATP to support protein secretion and intake of xylose and xylooligosaccharides. Additionally, several transporters for carbon uptake were identified in the genome of SirexAA-E by protein homology comparison with Streptomyces coelicolor , and several key transcriptional regulators used by SirexAA-E for catabolizing xylan were found by pull-down proteomics. The current study provides new insights into the extensive extracellular and intracellular responses of a cellulolytic Streptomyces to the major plant hemicellulose. IMPORTANCE Streptomyces sp. SirexAA-E can efficiently degrade cellulose, xylan, and mannan, the major polysaccharide components of woody biomass. Our previous work showed the relative simplicity of the secreted proteome used to degrade cellulose. In this study, we report on the extracellular and intracellular proteomic responses of SirexAA-E during growth on xylan. The substrate-specific proteomic profiles have given a new understanding of the regulation of xylanolytic enzymes and additional metabolic pathways supporting growth on a pentose sugar. These groupings of regulatory and structural proteins provide a blueprint for construction of more robust strains for biomass valorization.

  PublisherDOI

• A test of the variability vs. specificity hypotheses in the retention of a motor skill

  Human Movement Science · 2025-12-05

  articleSenior author
  PublisherDOI

Recent grants

• NIH Grant U54GM094584

  NIH · $9.5M · 2016

• NIH Grant P41RR002301

  NIH · $6.0M · 2015

• Protein-Protein Interaction Surfaces in Diiron Enzymes

  NSF · $807k · 2009–2013

• NIH Grant R01GM050853

  NIH · $2.6M · 2009

• Mechanisms of Action in Engineered Isoforms of the Diiron Toluene-4-Monooxygenase Complex

  NSF · $1.0M · 2003–2010

Frequent coauthors

• Taichi E. Takasuka

  Hokkaido University

  78 shared

• C.A. Bingman

  University of Wisconsin–Madison

  60 shared

• G.N. Phillips

  Rice University

  50 shared

• C.M. Bianchetti

  Great Lakes Bioenergy Research Center

  48 shared

• Eckard Münck

  Carnegie Mellon University

  45 shared

• Paul D. Adams

  Joint BioEnergy Institute

  42 shared

• John L. Markley

  University of Wisconsin–Madison

  40 shared

• Lai F. Bergeman

  Great Lakes Bioenergy Research Center

  36 shared

Labs

• Biochemistry Computational Research Facility (BCRF)PI

Education

• B.S., Biochemistry

  University of Wisconsin–Madison

  1990

• Ph.D., Biochemistry

  University of Wisconsin–Madison

  1995

Awards & honors

• Marvin J. Johnson Professor in Fermentation Biochemistry