1
|
Karanth S, Pradhan AK. Development of a novel machine learning-based weighted modeling approach to incorporate Salmonella enterica heterogeneity on a genetic scale in a dose-response modeling framework. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2023; 43:440-450. [PMID: 35413139 DOI: 10.1111/risa.13924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Estimating microbial dose-response is an important aspect of a food safety risk assessment. In recent years, there has been considerable interest to advance these models with potential incorporation of gene expression data. The aim of this study was to develop a novel machine learning model that considers the weights of expression of Salmonella genes that could be associated with illness, given exposure, in hosts. Here, an elastic net-based weighted Poisson regression method was proposed to identify Salmonella enterica genes that could be significantly associated with the illness response, irrespective of serovar. The best-fit elastic net model was obtained by 10-fold cross-validation. The best-fit elastic net model identified 33 gene expression-dose interaction terms that added to the predictability of the model. Of these, nine genes associated with Salmonella metabolism and virulence were found to be significant by the best-fit Poisson regression model (p < 0.05). This method could improve or redefine dose-response relationships for illness from relative proportions of significant genes from a microbial genetic dataset, which would help in refining endpoint and risk estimations.
Collapse
Affiliation(s)
- Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Abani K Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| |
Collapse
|
2
|
Nitrite Promotes ROS Production to Potentiate Cefoperazone-Sulbactam-Mediated Elimination to Lab-Evolved and Clinical-Evolved Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0232721. [PMID: 35863024 PMCID: PMC9430864 DOI: 10.1128/spectrum.02327-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cefoperazone-sulbactam (SCF)-resistant Pseudomonas aeruginosa poses a big challenge in the use of SCF to treat infection caused by the pathogen. We have recently shown exogenous nitrite-enabled killing of naturally and artificially evolved Pseudomonas aeruginosa strains (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) by SCF. However, the underlying mechanism is unknown. Here, reprogramming metabolomics was adopted to investigate how nitrite enhanced the SCF-mediated killing efficacy. Nitrite-reprogrammed metabolome displayed an activated pyruvate cycle (P cycle), which was confirmed by elevated activity of pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase, succinate dehydrogenase, and malate dehydrogenase. The activated P cycle provided NADH for the electron transport chain and thereby increased reactive oxygen species (ROS), which potentiated SCF to kill AP-RCLIN-EVO and AP-RLAB-EVO. The nitrite-enabled killing of AP-RCLIN-EVO and AP-RLAB-EVO by SCF was inhibited by PDH inhibitor furfural and ROS scavenger N-Acetyl-L-cysteine but promoted by ROS promoter Fe3+. SCF alone could not induce ROS, but SCF-mediated killing efficacy was enhanced by ROS. In addition, the present study demonstrated that nitrite repressed antioxidants, which were partly responsible for the elevated ROS. These results reveal a nitrite-reprogrammed metabolome mechanism by which AP-RCLIN-EVO and AP-RLAB-EVO sensitivity to SCF is elevated. IMPORTANCE Antibiotic-resistant Pseudomonas aeruginosa has become a real concern in hospital-acquired infections, especially in critically ill and immunocompromised patients. Understanding antibiotic resistance mechanisms and developing novel control measures are highly appreciated. We have recently shown that a reduced nitrite-dependent NO biosynthesis contributes to cefoperazone-sulbactam (SCF) resistance, which is reverted by exogenous nitrite, in both naturally and artificially evolved P. aeruginosa strains (AP-RCLIN-EVO and AP-RLAB-EVO, respectively). However, the mechanism is unknown. The present study reports that the nitrite-enabled killing of AP-RCLIN-EVO and AP-RLAB-EVO by SCF is attributed to the promoted production of reactive oxygen species (ROS). Nitrite activates the pyruvate cycle to generate NADH for the electron transport chain, which in turn promotes ROS generation. Nitrite-potentiated SCF-mediated killing is decreased by pyruvate dehydrogenase inhibitor furfural and ROS scavenger N-Acetyl-L-cysteine but increased by ROS promoter Fe3+. Furthermore, SCF-mediated killing is promoted by H2O2 in a dose-dependent manner. In addition, the combination of nitrite and H2O2 greatly enhances SCF-mediated killing. These results not only disclose a nitrite-ROS-potentiated SCF-mediated killing, but also show SCF-mediated killing is dependent upon ROS.
Collapse
|
3
|
Therapeutic Targets for Regulating Oxidative Damage Induced by Ischemia-Reperfusion Injury: A Study from a Pharmacological Perspective. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8624318. [PMID: 35450409 PMCID: PMC9017553 DOI: 10.1155/2022/8624318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 12/22/2022]
Abstract
Ischemia-reperfusion (I-R) injury is damage caused by restoring blood flow into ischemic tissues or organs. This complex and characteristic lesion accelerates cell death induced by signaling pathways such as apoptosis, necrosis, and even ferroptosis. In addition to the direct association between I-R and the release of reactive oxygen species and reactive nitrogen species, it is involved in developing mitochondrial oxidative damage. Thus, its mechanism plays a critical role via reactive species scavenging, calcium overload modulation, electron transport chain blocking, mitochondrial permeability transition pore activation, or noncoding RNA transcription. Other receptors and molecules reduce tissue and organ damage caused by this pathology and other related diseases. These molecular targets have been gradually discovered and have essential roles in I-R resolution. Therefore, the current study is aimed at highlighting the importance of these discoveries. In this review, we inquire about the oxidative damage receptors that are relevant to reducing the damage induced by oxidative stress associated with I-R. Several complications on surgical techniques and pathology interventions do not mitigate the damage caused by I-R. Nevertheless, these therapies developed using alternative targets could work as coadjuvants in tissue transplants or I-R-related pathologies
Collapse
|
4
|
Canpolat G, Dolak İ, Onat R, Keçili R, Baysal Z, Ziyadanoğulları B, Ersöz A, Say R. Development of molecular imprinting-based smart cryogels for selective recognition and separation of serum cytochrome-c as a biochemical indicator. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
5
|
Fan J, Gao Z, Zhao DP, Wang P, Wu ZZ, Li XM. Effects of nitric oxide donor N,N'-di-sec-butyl-N,N'-dinitroso-1,4-phenylenediamine on the expression of interferon-gamma in tumor infiltrating lymphocytes. Med Gas Res 2020; 9:171-175. [PMID: 31898601 PMCID: PMC7802422 DOI: 10.4103/2045-9912.273954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Nitric oxide (NO) has been proven to be a key regulator in the mammalian immune response, such as the innate and adaptive immune responses to tumors. The messenger NO involves T helper cell differentiation and lymphocyte biofunctions. In this study, we employed N,N’-di-sec-butyl-N,N’-dinitroso-1,4-phenylenediamine as NO donor and released NO around tumor infiltrating lymphocytes in vitro by short-time blue light irradiation. The interferon-γ secretion of tumor infiltrating lymphocytes was investigated to study the functional changes caused by the accurate spatio-temporal delivery of NO. The downregulation of interferon-γ in tumor infiltrating lymphocytes after NO treatment indicates promising biological applications to potentially play a role in the treatment of autoimmune diseases. The study was approved by the Medical Ethics Committee of the Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, China (approved No. 065) on February 12, 2018.
Collapse
Affiliation(s)
- Jing Fan
- Department of Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen; The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou; Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong Province, China
| | - Zhen Gao
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou; Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong Province, China
| | - De-Peng Zhao
- Department of Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Ping Wang
- Department of Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Zheng-Zhong Wu
- Department of Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Xue-Mei Li
- Department of Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| |
Collapse
|
6
|
Feng J, Luo L, Liu Y, Fu S, Chen J, Duan X, Xiang L, Zhang Y, Wu J, Fan J, Wen Q, Zhang Y, Yang J, Peng J, Zhao M, Yang L. TP53-induced glycolysis and apoptosis regulator is indispensable for mitochondria quality control and degradation following damage. Oncol Lett 2018; 15:155-160. [PMID: 29375708 PMCID: PMC5766069 DOI: 10.3892/ol.2017.7303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/22/2017] [Indexed: 11/06/2022] Open
Abstract
Mitochondria have been described as 'the powerhouse of the cell' as the organelle generates the majority of adenosine triphosphate (ATP) in cells to support life. Mitochondria can be damaged due to stress, for example by reactive oxygen species (ROS). TP53-induced glycolysis and apoptosis regulator (TIGAR) serves a role in suppressing ROS damage and may protect mitochondria integrity. In the present study, the localization of TIGAR on mitochondria in 5-8F cells was demonstrated. Furthermore, it was indicated that the knockdown of TIGAR using lentivirus-short hairpin RNA induces the loss of mitochondrial membrane potential and cytochrome c leakage. However, these damaged mitochondria were not degraded in cells, but exhibited an abnormal appearance as indicated by mitochondrial swelling, crista collapse and vacuolization, with physiological dysfunction marked by reduced ATP production. Therefore, TIGAR maybe an indispensable protein for mitochondrial protection and degradation following cellular damage.
Collapse
Affiliation(s)
- Jing Feng
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Li Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yong Liu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Shaozhi Fu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jie Chen
- Department of Rheumatology and Immunology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xiaoxia Duan
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Li Xiang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yanling Zhang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jinbo Wu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Juan Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Ye Zhang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jingpin Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jinxia Peng
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Ming Zhao
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Linglin Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| |
Collapse
|
7
|
Zhu H, Jin Q, Li Y, Ma Q, Wang J, Li D, Zhou H, Chen Y. Melatonin protected cardiac microvascular endothelial cells against oxidative stress injury via suppression of IP3R-[Ca 2+]c/VDAC-[Ca 2+]m axis by activation of MAPK/ERK signaling pathway. Cell Stress Chaperones 2018; 23:101-113. [PMID: 28669047 PMCID: PMC5741585 DOI: 10.1007/s12192-017-0827-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/14/2017] [Accepted: 06/21/2017] [Indexed: 10/19/2022] Open
Abstract
The cardiac microvascular reperfusion injury is characterized by the microvascular endothelial cells (CMECs) oxidative damage which is responsible for the progression of cardiac dysfunction. However, few strategies are available to reverse such pathologies. This study aimed to explore the mechanism by which oxidative stress induced CMECs death and the beneficial actions of melatonin on CMECs survival, with a special focused on IP3R-[Ca2+]c/VDAC-[Ca2+]m damage axis and the MAPK/ERK survival signaling. We found that oxidative stress induced by H2O2 significantly activated cAMP response element binding protein (CREB) that enhanced IP3R and VDAC transcription and expression, leading to [Ca2+]c and [Ca2+]m overload. High concentration of [Ca2+]m suppressed ΔΨm, opened mPTP, and released cyt-c into cytoplasm where it activated mitochondria-dependent death pathway. However, melatonin could protect CMECs against oxidative stress injury via stimulation of MAPK/ERK that inactivated CREB and therefore blocked IP3R/VDAC upregulation and [Ca2+]c/[Ca2+]m overload, sustaining mitochondrial structural and function integrity and ultimately blockading mitochondrial-mediated cellular death. In summary, these findings confirmed the mechanisms by which oxidative injury induced CMECs mitochondrial-involved death and provided an attractive and effective way to enhance CMECs survival.
Collapse
Affiliation(s)
- Hang Zhu
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China
| | - Qinhua Jin
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China
| | - Yang Li
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China
| | - Qiang Ma
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China
| | - Jing Wang
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China
| | - Dandan Li
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China
| | - Hao Zhou
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China.
| | - Yundai Chen
- Department of Cardiology, Chinese PLA General Hospital, #28 Fuxing Rd, Beijing, 100853, China.
| |
Collapse
|
8
|
Ascenzi P, Coletta M, Wilson MT, Fiorucci L, Marino M, Polticelli F, Sinibaldi F, Santucci R. Cardiolipin-cytochrome c complex: Switching cytochrome c from an electron-transfer shuttle to a myoglobin- and a peroxidase-like heme-protein. IUBMB Life 2015; 67:98-109. [PMID: 25857294 DOI: 10.1002/iub.1350] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/11/2015] [Indexed: 12/18/2022]
Abstract
Cytochrome c (cytc) is a small heme-protein located in the space between the inner and the outer membrane of the mitochondrion that transfers electrons from cytc-reductase to cytc-oxidase. The hexa-coordinated heme-Fe atom of cytc displays a very low reactivity toward ligands and does not exhibit significant catalytic properties. However, upon cardiolipin (CL) binding, cytc achieves ligand binding and catalytic properties reminiscent of those of myoglobin and peroxidase. In particular, the peroxidase activity of the cardiolipin-cytochrome c complex (CL-cytc) is critical for the redistribution of CL from the inner to the outer mitochondrial membranes and is essential for the execution and completion of the apoptotic program. On the other hand, the capability of CL-cytc to bind NO and CO and the heme-Fe-based scavenging of reactive nitrogen and oxygen species may affect apoptosis. Here, the ligand binding and catalytic properties of CL-cytc are analyzed in parallel with those of CL-free cytc, myoglobin, and peroxidase to dissect the potential mechanisms of CL in modulating the pro- and anti-apoptotic actions of cytc.
Collapse
Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Roma, Italy
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
Collapse
|