Browsing by Author "Wang, Z"

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    Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics.
    (Journal of proteome research, 2012-02) Yang, W; Thompson, JW; Wang, Z; Wang, L; Sheng, H; Foster, MW; Moseley, MA; Paschen, W
    Transient cerebral ischemia dramatically activates small ubiquitin-like modifier (SUMO2/3) conjugation. In cells exposed to 6 h of transient oxygen/glucose deprivation (OGD), a model of ischemia, SUMOylation increases profoundly between 0 and 30 min following re-oxygenation. To elucidate the effect of transient OGD on SUMO conjugation of target proteins, we exposed neuroblastoma B35 cells expressing HA-SUMO3 to transient OGD and used stable isotope labeling with amino acids in cell culture (SILAC) to quantify OGD-induced changes in levels of specific SUMOylated proteins. Lysates from control and OGD-treated cells were mixed equally, and HA-tagged proteins were immunoprecipitated and analyzed by 1D-SDS-PAGE-LC-MS/MS. We identified 188 putative SUMO3-conjugated proteins, including numerous transcription factors and coregulators, and PIAS2 and PIAS4 SUMO ligases, of which 22 were increased or decreased more than ±2-fold. In addition to SUMO3, the levels of protein-conjugated SUMO1 and SUMO2, as well as ubiquitin, were all increased. Importantly, protein ubiquitination induced by OGD was completely blocked by gene silencing of SUMO2/3. Collectively, these results suggest several mechanisms for OGD-modulated SUMOylation, point to a number of signaling pathways that may be targets of SUMO-based signaling and recovery from ischemic stress, and demonstrate a tightly controlled crosstalk between the SUMO and ubiquitin conjugation pathways.
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    Can International Climate Cooperation Induce Knowledge Spillover to Developing Countries? Evidence from CDM
    (Environmental and Resource Economics, 2022-08-01) Cui, J; Wang, Z; Yu, H
    Under the Kyoto Protocol, the Clean Development Mechanism (CDM) expects to facilitate the North-South knowledge spillovers for climate-friendly technologies. This paper examines the effect of this voluntary international climate cooperation on firm innovation and knowledge spillovers through the lens of CDM projects in China. Using a matched Difference-in-Differences (DID) approach, we find that CDM projects contribute to firms’ innovation quantity, quality, and direction in renewable energy and energy efficiency technologies. These effects are more pronounced in inducing wind, hydro, and solar energy. We explore the role of foreign sponsors in knowledge spillovers. Sponsoring firms play the technology supplier role by raising the innovation quantity and quality, while sponsoring governments perform the information intermediary role by facilitating citation flows.
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    Correction to: AI is a viable alternative to high throughput screening: a 318-target study (Scientific Reports, (2024), 14, 1, (7526), 10.1038/s41598-024-54655-z)
    (Scientific Reports, 2024-12-01) Giles, E; Heifets, A; Artía, Z; Inde, Z; Liu, Z; Zhang, Z; Wang, Z; Su, Z; Chung, Z; Frangos, ZJ; Li, Y; Yen, Y; Sidorova, YA; Tse-Dinh, YC; He, Y; Tang, Y; Li, Y; Pérez-Pertejo, Y; Gupta, YK; Zhu, Y; Sun, Y; Li, Y; Chen, Y; Aldhamen, YA; Hu, Y; Zhang, YJ; Zhang, X; Yuan, X; Wang, X; Qin, X; Yu, X; Xu, X; Qi, X; Lu, X; Wu, X; Blanchet, X; Foong, WE; Bradshaw, WJ; Gerwick, WH; Kerr, WG; Hahn, WC; Donaldson, WA; Van Voorhis, WC; Zhang, W; Tang, W; Li, W; Houry, WA; Lowther, WT; Clayton, WB; Van Hung Le, V; Ronchi, VP; Woods, VA; Scoffone, VC; Maltarollo, VG; Dolce, V; Maranda, V; Segers, VFM; Namasivayam, V; Gunasekharan, V; Robinson, VL; Banerji, V; Tandon, V; Thai, VC; Pai, VP; Desai, UR; Baumann, U; Chou, TF; Chou, T; O’Mara, TA; Banjo, T; Su, T; Lan, T; Ogunwa, TH; Hermle, T; Corson, TW; O’Meara, TR; Kotzé, TJ; Herdendorf, TJ; Richardson, TI; Kampourakis, T; Gillingwater, TH; Jayasinghe, TD; Teixeira, TR; Ikegami, T; Moreda, TL; Haikarainen, T; Akopian, T; Abaffy, T; Swart, T; Mehlman, T; Teramoto, T; Azeem, SM; Dallman, S; Brady-Kalnay, SM; Sarilla, S; Van Doren, SR; Marx, SO; Olson, SH; Poirier, S; Waggoner, SN
    Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-024-54655-z, published online 02 April 2024 The original version of this Article contained errors. In the original version of this article, Ellie Giles was omitted from the Author list. Additionally, the following Affiliation information has been updated: 1. Affiliation 25 was incorrect. Affiliation 25 ‘Queensland University of Technology, Brisbane, USA.’ now reads, ‘Queensland University of Technology, Brisbane, Australia.’ 2. Marta Giorgis was incorrectly affiliated with the ‘University of Aberdeen, Aberdeen, UK.’ The correct Affiliation is listed below: ‘University of Turin, Turin, Italy.’ 3. Affiliations 52, 125 and 261 were duplicated. As a result, the correct Affiliation for Andrew B. Herr, Benjamin Liou, David A. Hildeman, Joseph J. Maciag, Ying Sun, Durga Krishnamurthy, and Stephen N. Waggoner is: ‘Cincinnati Children’s Hospital Medical Center, Cincinnati, USA.’ Furthermore, an outdated version of Figure 1 was typeset. The original Figure 1 and accompanying legend appear below. (Figure presented.) Pairs of representative compounds extracted from AI patents (right) and corresponding prior patents (left) for clinical-stage programs (CDK792,93, A2Ar-antagonist94,95, MALT196,97, QPCTL98,99, USP1100,101, and 3CLpro102,103). The identical atoms between the chemical structures are highlighted in red. Lastly, The Acknowledgements section contained an error. “See Supplementary section S1.” now reads, “See Supplementary section S2.” The original Article has been corrected.
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    Development of a simplified spinal cord ischemia model in mice.
    (Journal of neuroscience methods, 2010-06) Wang, Z; Yang, W; Britz, GW; Lombard, FW; Warner, DS; Sheng, H
    Use of genetically manipulated mice facilitates understanding pathological mechanisms in many diseases and contributes to therapy development. However, there is no practical and clinically relevant mouse model available for spinal cord ischemia. This report introduces a simplified long-term outcome mouse model of spinal cord ischemia. Male C57Bl/6J mice were anesthetized with isoflurane and endotracheally intubated. The middle segment of the thoracic aorta was clamped for 0, 8, 10 or 12 min via left lateral thoracotomy. Rectal temperature was maintained at 37.0+/-0.5 degrees C. A laser Doppler probe was used to measure lumbar spinal cord blood flow during thoracic aorta cross-clamping. Open field locomotor function and rotarod performance were evaluated at 1h and 1, 3, 5, and 7 days post-injury. Surviving neurons in the lumbar ventral horn were counted at 7 days post-injury. Cross-clamping the middle segment of the thoracic aorta resulted in approximately 90% blood flow reduction in the lumbar spinal cord. Neurological deficit and neuronal cell death were associated with ischemia duration. Another set of mice were subjected to 10 min aortic clamping or sham surgery and neurological function was examined at 1h and 1, 3, 5, 7, 14, and 28 days. Four of 5 mice (80%) in the injured group survived 28 days and had significant neurological deficit. This study indicates that cross-clamping of the aorta via left thoracotomy is a simple and reliable method to induce spinal cord ischemia in mice allowing definition of long-term outcome.
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    Imaging system QA of a medical accelerator, Novalis Tx, for IGRT per TG 142: our 1 year experience.
    (Journal of applied clinical medical physics, 2012-07-05) Chang, Z; Bowsher, J; Cai, J; Yoo, S; Wang, Z; Adamson, J; Ren, L; Yin, FF
    American Association of Physicists in Medicine (AAPM) task group (TG) 142 has recently published a report to update recommendations of the AAPM TG 40 report and add new recommendations concerning medical accelerators in the era of image-guided radiation therapy (IGRT). The recommendations of AAPM TG 142 on IGRT are timely. In our institute, we established a comprehensive imaging QA program on a medical accelerator based on AAPM TG 142 and implemented it successfully. In this paper, we share our one-year experience and performance evaluation of an OBI capable linear accelerator, Novalis Tx, per TG 142 guidelines.
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    Single-Fraction Radiosurgery for 4 or More Brain Metastases.
    (International journal of radiation oncology, biology, physics, 2016-10) Limon, D; Kim, GJ; McSherry, F; Herndon, J; Fecci, PE; Adamson, J; Sampson, JH; Floyd, SR; Wang, Z; Vlahovic, G; Yin, FF; Kirkpatrick, JP
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    Small molecule delivery across a perforated artificial membrane by thermoreversible hydrogel poloxamer 407.
    (Colloids and surfaces. B, Biointerfaces, 2019-10) Santimetaneedol, A; Wang, Z; Arteaga, DN; Aksit, A; Prevoteau, C; Yu, M; Chiang, H; Fafalis, D; Lalwani, AK; Kysar, JW
    Microperforations in the round window membrane have been suggested for enhancing the rate and reliability of drug delivery into the cochlea. Intratympanic injection, the most common delivery method, involves injecting therapy into the middle ear to establish a reservoir from which drug diffuses across the round window membrane into the cochlea. This process is highly variable because (i) the reservoir, if liquid, can lose contact with the membrane and (ii) diffusion across the membrane is intrinsically variable even with a stable reservoir. To address these respective sources of variability, we compared the thermoreversible hydrogel poloxamer 407 (P407) to saline as a drug carrier and studied the effect of membrane microperforations on drug diffusion rate. We used Rhodamine B as a drug proxy to measure permeance across an artificial membrane in a horizontal diffusion cell. We found that permeance of Rhodamine B from a saline reservoir was an order of magnitude higher than that from a P407 reservoir across unperforated membranes. Moreover, permeance increased with total perforation cross-sectional area regardless of number of perforations (p < 0.05 for all saline-based experiments), but the same association was not found with P407. Rather, for a P407 reservoir, only a large perforation increased permeance (p < 0.001), while multiple small perforations did not (p = 0.749). These results confirm that for drug dissolved in saline, multiple small perforations can effectively enhance diffusion. However, for drug dissolved in P407, larger perforations are necessary.
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    Technological forecasting & social change does environmental regulation induce green innovation? a panel study of Chinese listed firms
    (Technological Forecasting and Social Change, 2022-03-01) Cui, J; Dai, J; Wang, Z; Zhao, X
    To promote cleaner production, China launched nation-wide Cleaner Production Audit (CPA) program in 2004. This study examines the “weak” version of the Porter hypothesis while focusing on Chinese listed firms from 1990 to 2010. In this study, we provided evidence on the influence of China's CPA program on innovation based on green patent data. Using a difference-in-difference (DID) method, we find that there is a positive regulation effect on green innovation, i.e. the “weak” Porter hypothesis has been realized in the CPA program in China. Moreover, our results suggest that the regulation effect is more pronounced in encouraging radical green innovations measured by environmental invention patents than incremental green innovation measured by environmental utility patents. Then, we find that the CPA program regulatory effect is also affected by moderation variables such as industrial pollution intensity, but not by firm ownership. Our findings shed light on the policy implications on how firms respond to environmental regulations.
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    The full configuration interaction quantum Monte Carlo method in the lens of inexact power iteration
    (2018-02-14) Lu, J; Wang, Z
    In this paper, we propose a general analysis framework for inexact power iteration, which can be used to efficiently solve high dimensional eigenvalue problems arising from quantum many-body problems. Under the proposed framework, we establish the convergence theorems for several recently proposed randomized algorithms, including the full configuration interaction quantum Monte Carlo (FCIQMC) and the fast randomized iteration (FRI). The analysis is consistent with numerical experiments for physical systems such as Hubbard model and small chemical molecules. We also compare the algorithms both in convergence analysis and numerical results.
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    Transient ischemia induces massive nuclear accumulation of SUMO2/3-conjugated proteins in spinal cord neurons.
    (Spinal cord, 2013-02) Wang, Z; Wang, R; Sheng, H; Sheng, SP; Paschen, W; Yang, W

    Objectives

    The objective of this study is to determine whether transient spinal cord ischemia activates small ubiquitin-like modifier (SUMO1-3) conjugation, a post-translational protein modification that protects neurons from ischemia-like conditions.

    Methods

    Mice were subjected to 8-12 min of spinal cord ischemia and 3-24 h of recovery using a newly developed experimental model. To characterize the model, activation of stress response pathways induced after spinal cord ischemia, previously observed in other experimental models, was verified by western blot analysis. Levels and subcellular localization of SUMO-conjugated proteins in spinal cords were evaluated by western blot analysis and immunohistochemistry, respectively.

    Results

    Following transient spinal cord ischemia, stress responses were activated as indicated by increased phosphorylation of eukaryotic initiation factor 2 (eIF2α), extracellular signal-regulated kinases (ERK1/2) and Akt. SUMO1 conjugation was not altered, but a selective rise in levels of SUMO2/3-conjugated proteins occurred, peaking at 6 h reperfusion. The marked activation of SUMO2/3 conjugation was a neuronal response to ischemia, as indicated by co-localization with the neuronal marker NeuN, and was associated with nuclear accumulation of SUMO2/3-conjugated proteins.

    Conclusion

    Our study suggests that spinal cord neurons respond to ischemic stress by activation of SUMO2/3 conjugation. Many of the identified SUMO target proteins are transcription factors and other nuclear proteins involved in gene expression and genome stability. It is therefore concluded that the post-ischemic activation of SUMO2/3 conjugation may define the fate of neurons exposed to a transient interruption of blood supply, and that this pathway could be a therapeutic target to increase the resistance of spinal cord neurons to transient ischemia.
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    Water quality implications of the neutralization of acid mine drainage with coal fly ash from India and the United States
    (Fuel, 2022-12-15) Weinberg, R; Coyte, R; Wang, Z; Das, D; Vengosh, A
    Subsurface coal mining often induces the formation of acid mine drainage (AMD) in active and abandoned coal mines while coal combustion generates coal combustion residuals (CCR), including fly ash (FA), with elevated levels of toxic metals. Decades of AMD and CCR production have caused major environmental and human health impacts. Given the typically elevated level of oxides in FA, previous studies have examined its potential to neutralize AMD and remove the associated metals. While the neutralization of AMD through reaction with FA has been demonstrated to successfully remove cationic metals, the fate of oxyanion forming elements are less well studied and is the focus of this study. Here we conducted 49 different experiments in which simulated AMD solutions were interacted with representative U.S. (n = 7) and Indian (n = 6) FA samples through controlled liquid to solid ratios in short-term (24 h) and long-term (up to 5 weeks) lab-scale experiments. We show that Class-F FA, originating from Gondwana and Northeastern Tertiary coals in India, has limited neutralization capacity, while Class-C FA, with high CaO and MgO contents from Powder River coals in the U.S. has the greatest AMD neutralization capacity among the studied fly ashes. The neutralization experiments show that AMD-FA reactions cause the removal of cationic elements (i.e., Fe, Mn, and Al) from solution, while at the same time, leaching oxyanion forming elements (i.e., As, Se, Mo, Cr, B, Tl, and Sb) from the FA, increasing the potential environmental risks from the treated leachates. The magnitude of mobilization of these elements depends on their concentrations in the FA and the pH conditions. We show that using FA from the Appalachian and Illinois coals efficiently neutralizes AMD, but also results in secondary contamination of the treated effluents with oxyanion forming elements to levels exceeding drinking water and ecological standards, which could contaminate the ambient environment, whereas neuralization with Powder River Basin Class-C FA induces only limited contamination.