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Wu, Wenting

Publications and source records attributed to Wu, Wenting.

13 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multi-omics data resource: Data package 22 (Pck022)

In type 1 diabetes (T1D), autoimmune response and inflammation cause the death of pancreatic ß cells, leading to the body’s inability to produce insulin and maintain glucose homeostasis. This process is at least in part mediated by pro-inflammatory cytokines, such as interferon (IFN)a, IFN?, interleukin (IL)-1ß, and tumor necrosis factor (TNF)a, which induce ß-cell dysfunction and apoptosis. A deep understanding of the ß-cell signaling and regulatory networks induced by these cytokines could lead to the identification of therapeutic targets to prevent T1D development. To study cytokine-mediated islets/ß-cell signaling and regulatory networks, a variety of omics experiments have been conducted, including transcriptomics, epigenomics (DNA methylation, UMI-4C, ATAC-seq & ChIP-seq), proteomics (bottom-up, top-down, post-translational modification analysis), lipidomics, and metabolomics. The combination of these datasets can be instrumental in identifying signaling components and regulatory factors involved in ß-cell stress/death. Here, we aggregated these multiple omics datasets into a centralized location, providing a quality-controlled and statistically rigorous resource for investigators seeking to holistically study ß-cell regulation by pro-inflammatory cytokines. The data package consists of isolated pancreatic islets from adult male C57BL6/J mice treated with IL-1β, IFNγ or IL-1β + IFNγ for 6 h and submitted for scRNA-seq. This study focused on understanding the heterogeneity of the cytokine-mediated response. Data contributors: Jennifer S Stancill & John A Corbett: Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA Data repository: GSE156175 Publication: 10.26508/lsa.202000949

Sarkar, Soumyadeep [Pacific Northwest National Lab↗
DOE OSTI2026

Multi-omics data resource: Data package 23 (Pck023)

The data package consists of isolated pancreatic islets from adult male C57BL6/J mice treated with IL-1β + IFNγ, IL-1β + IFNγ + NMMA, or NMMA alone for 18 h and submitted for scRNA-seq. This study focused on the cell-type-specific effects of nitric oxide signaling in islets and characterized the heterogeneity of responses. Data contributors: Jennifer S Stancill & John A Corbett: Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA Data repository: GSE183010 Publication: 10.1093/function/zqab063

Sarkar, Soumyadeep [Pacific Northwest National Lab↗
DOE OSTI2026

Multi-omics data resource: Data package 24 (Pck024)

The data package consists of isolated pancreatic islets from 3 human donors treated with IL-1β, IFNγ or IL-1β + IFNγ for 6 h and IL-1β, IFNγ, IL-1β + IFNγ, IL-1β + IFNγ + NMMA or NMMA for 18 h and submitted for scRNA-seq. This study examines cytokine-stimulated changes in gene expression in human islets using single-cell RNA sequencing. Data contributors: Jennifer S Stancill & John A Corbett: Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA Data repository: GSE251730 Publication: 10.1093/function/zqae015

Sarkar, Soumyadeep [Pacific Northwest National Lab↗
DOE OSTI2026

Multi-omics data resource: Data package 25 (Pck025)

This data package comprises omics datasets from human pancreatic islets treated with IL-1β + IFNγ or with estrogen (E2) for 18 h. Two RNA-seq datasets are available: the first is a discovery dataset involving human islets treated with or without IL-1β + IFNγ for 18 hours; the second is a validation dataset, where human islets are treated with or without IL-1β + IFNγ or E2 for 18 hours. DIA proteomic analysis was performed on the same validation dataset samples. Data contributors: Kiersten L. Webster, Sarah Tersey & Raghavendra G. Mirmir: Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA. Soumyadeep Sarkar, Raghavendra Mirmira, Ernesto S. Nakayasu: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA. Data repository: RNA-seq: GSE310965 Proteomics: MSV000101892 Publication: PMID 41279069

Sarkar, Soumyadeep [Pacific Northwest National Lab↗
DOE OSTI2024

RNA Splicing Events in Circulation Distinguish Individuals With and Without New-onset Type 1 Diabetes

Context: Alterations in RNA splicing may influence protein isoform diversity that contributes to or reflects the pathophysiology of certain diseases. Whereas specific RNA splicing events in pancreatic islets have been investigated in models of inflammation in vitro, how RNA splicing in the circulation correlates with or is reflective of type 1 diabetes (T1D) disease pathophysiology in humans remains unexplored. Objective: To use machine learning to investigate if alternative RNA splicing events differ between individuals with and without new-onset T1D and to determine if these splicing events provide insight into T1D pathophysiology. Methods: RNA deep sequencing was performed on whole blood samples from 2 independent cohorts: a training cohort consisting of 12 individuals with new-onset T1D and 12 age- and sex-matched nondiabetic controls and a validation cohort of the same size and demographics. Machine learning analysis was used to identify specific isoforms that could distinguish individuals with T1D from controls. Results: Distinct patterns of RNA splicing differentiated participants with T1D from unaffected controls. Notably, certain splicing events, particularly involving retained introns, showed significant association with T1D. Machine learning analysis using these splicing events as features from the training cohort demonstrated high accuracy in distinguishing between T1D subjects and controls in the validation cohort. Gene Ontology pathway enrichment analysis of the retained intron category showed evidence for a systemic viral response in T1D subjects. Conclusion: Alternative RNA splicing events in whole blood are significantly enriched in individuals with new-onset T1D and can effectively distinguish these individuals from unaffected controls. Further, our findings also suggest that RNA splicing profiles offer the potential to provide insights into disease pathogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Human Islet Research Network (HIRN): Alternative Splicing Events

Inclusion levels of alternative splicing (AS) events of five different varieties (i.e. skipped exon (SE), retained intron (RI), alternative 5’ splice site (A5SS), alternative 3’ splice site (A3SS), and mutually exclusive exons (MXE)) were measured in human blood samples from two separate cohorts of patients. Cohort 1 (Training Cohort): 12 healthy controls; 12 new onset type 1 diabetic (T1D) cases cases and controls matched on biological sex, age, and body mass index (BMI) 180 million reads Cohort 2 (Testing Cohort): 12 healthy controls; 12 new onset type 1 diabetic (T1D) cases cases and controls matched on biological sex and age. BMI not recorded. 150 million reads

Webb-Robertson, Bobbie-Jo M↗
DOE OSTI2023

Alternative Splicing Events

Inclusion levels of alternative splicing (AS) events of five different varieties (i.e. skipped exon (SE), retained intron (RI), alternative 5’ splice site (A5SS), alternative 3’ splice site (A3SS), and mutually exclusive exons (MXE)) were measured in human blood samples from two separate cohorts of patients. Cohort 1 (Training Cohort): 12 healthy controls; 12 new onset type 1 diabetic (T1D) cases cases and controls matched on biological sex, age, and body mass index (BMI) 180 million reads Cohort 2 (Testing Cohort): 12 healthy controls; 12 new onset type 1 diabetic (T1D) cases cases and controls matched on biological sex and age. BMI not recorded. 150 million reads

Webb-Robertson, Bobbie-Jo M↗
DOE OSTI2023

Single and dual metal atom catalysts for enhanced singlet oxygen generation and oxygen reduction reaction

We demonstrate rational design of graphene-supported single and dual metal atom catalysts (SACs and DACs) for photocatalytic applications, such as singlet oxygen ( 1 O 2 ) sensitization and H 2 O 2 production. Here we combine density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations with experimental verifications. We found a synergistic effect between triplet sensitization and triplet–triplet (Dexter) energy transfer; both play a role in the photocatalytic activity through the volcano plot of 3d transition metal SACs. More specifically, FeN 4 -SAC exhibits a low ISC energy gap (ΔE ISC ) of 0.039 eV, compared with 0.108 eV for FeNiN8-DACs, both possessing a high Bader charge transfer of 0.366 e- and 0.405 e-, respectively. Guided by these computational results, we synthesized a series of SACs and a DAC and confirmed their structures with scanning transmission electron microscopy (STEM) along with the X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). We then confirm their band structures with low-energy inverse photoemission spectroscopy (LEIPS) and UV-vis-NIR. Subsequently, we synthesized the catalysts for the photooxygenation of anthracene and two-electron oxygen reduction reaction (ORR) to measure their photocatalytic activity. We found that H 2 O 2 production through the two-electron ORR competes with the 1 O 2 generation through Dexter energy transfer. FeN 4 -SAC demonstrates a high photooxygenation conversion of 86% and a high 1 O 2 quantum yield of 1.04, obtained from electron spin resonance (ESR) spectroscopy, with low H 2 O 2 production. In contrast, NiN 4 -SAC exhibits a low 1 O 2 generation and a high H 2 O 2 production mainly because of the high Gibbs free energy of the OOH* intermediate. In conclusion, this work proposes an effective DFT-guided strategy for designing SACs and DACs for various photocatalytic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Non-bonding interaction of dual atom catalysts for enhanced oxygen reduction reaction

Here, we demonstrate the design of graphene-supported dual atom catalysts (DACs) for the four-electron oxygen reduction reaction (ORR), by utilizing the non-bonding interaction of counterpart metals (M) that synergistically tune the electronic properties and catalytic activity of the Fe active site in FeMN 6 -DAC and FeMN 8 -DAC systems, where M stands for Fe, Co, Ni, Cu, and Zn. More specifically, for Fe-M distances below 15Å, the non-bonding interaction is significant, making the system act as the DAC. We predicted that FeNiN 6 -DAC and FeNiN 8 -DAC exhibit a low ORR overpotential (η ORR ) of 0.28 V and 0.47 V, respectively, which are at the summits of volcano plots. This low η ORR originates from the high Bader charge transfer coupled with high spin density at the Fe site in both the FeNiN 6 -DAC and FeNiN 8 -DAC systems, which weakens the adsorption of OH* intermediate while enhancing its desorption to H 2 O. Guided by these density functional theory (DFT) computational results, we synthesized FeCoN 8 -DAC and FeNiN 8 -DAC along with N-doped graphene and confirmed their structures with scanning transmission electron microscopy (STEM), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and electron spin resonance (ESR). We verify experimentally the catalytic activities and find that FeNiN 8 -DAC has the low experimental overpotential of 0.39 V with a Tafel slope of 47 mVdec -1 . Based on these results, we propose a DFT-guided strategy to tune the charge transfer and spin population of the active site toward designing DACs for electrochemical ORR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Tracking the environmental impacts of ecological engineering on coastal wetlands with numerical modeling and remote sensing

Coastal wetlands are the most valuable ecosystems on the earth but facing severe degradation and losses owing to climate change and anthropogenic activities. Many ecological engineering projects (EEP) have been conducted to mitigate the degradation of coastal wetlands. However, the geomorphological impacts of EEP on coastal wetlands have not been well documented. In this study, a method employed a process-based hydrodynamic model and remote sensing (RS) was developed to evaluate the impacts of EEP on the geomorphological change of a prototype Ramsar site. Results demonstrated that RS has great potential in improving the quality of bathymetry data for the numerical model with a decrease of RMSE from 0.52 m to 0.3 m. It also showed good capacity in trend detection of geomorphological change spatially. Results showed the Chongming Dongtan wetland experienced erosion with an annual rate of -0.035 m/yr from 2013 to 2016 after the implementation of EEP. The deposition rate changed significantly in the area within 200 m of the EEP. It is found that the EEP modified the composition of vegetation, sediment transportation, as well as substrate stability, affecting the geomorphological change of coastal wetlands. It is suggested that the EEP with moderate anthropogenic disturbance is a direct and effective way to recover the coastal habitats for waterbirds. However, the modification of the coastal wetland ecosystem by EEP will lead to the potential vulnerability to global climate change. Therefore, how to mitigate the advantages and disadvantages of the EEP is needed to be further studied to find a more sustainable way for coastal management.

geomorphological change, coastal wetlands, Ecologi↗
DOE OSTI2021

Integrated modeling analysis of estuarine responses to extreme hydrological events and sea-level rise

Estuaries are vulnerable to climate change and are particularly sensitive to extreme river discharge (RD) and sea-level rise (SLR). To understand the effects of extreme RD and SLR on estuaries, an integrated modeling approach is adopted to simulate hydrodynamic changes in the Yangtze River Estuary. Model results showed that SLR will intensify the estuarine hydrodynamics in water level, currents, and salinity. Water level, current speed, and salinity increased linearly with the magnitude of SLR. The hydrological model suggested a lower RD in the future. This will increase the saltwater intrusion, which will be more severe during the lower RD and drought extreme hydrological event (EHE) conditions. Model results also suggested that the saltwater intrusion is more sensitive to RD than SLR. In addition, the interplay between the RD and SLR will exacerbate the impacts of coastal oceans on estuarine hydrodynamics, especially during extremely low RD conditions. Moreover, the decrease of RD and deepening of the channel due to human activities will also amplify the effects of SLR on the Estuary, increasing the risk of coastal disasters.

3-D hydrodynamic model, extreme climate, draught, ↗