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Carrera-Escalé L, Benali A, Rathert AC, Martín-Pinardel R, Bernal-Morales C, Alé-Chilet A, Barraso M, Marín-Martinez S, Feu-Basilio S, Rosinés-Fonoll J, Hernandez T, Vilá I, Castro-Dominguez R, Oliva C, Vinagre I, Ortega E, Gimenez M, Vellido A, Romero E, Zarranz-Ventura J. Radiomics-Based Assessment of OCT Angiography Images for Diabetic Retinopathy Diagnosis. Ophthalmol Sci 2022; 3:100259. [PMID: 36578904 PMCID: PMC9791596 DOI: 10.1016/j.xops.2022.100259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
Purpose To evaluate the diagnostic accuracy of machine learning (ML) techniques applied to radiomic features extracted from OCT and OCT angiography (OCTA) images for diabetes mellitus (DM), diabetic retinopathy (DR), and referable DR (R-DR) diagnosis. Design Cross-sectional analysis of a retinal image dataset from a previous prospective OCTA study (ClinicalTrials.govNCT03422965). Participants Patients with type 1 DM and controls included in the progenitor study. Methods Radiomic features were extracted from fundus retinographies, OCT, and OCTA images in each study eye. Logistic regression, linear discriminant analysis, support vector classifier (SVC)-linear, SVC-radial basis function, and random forest models were created to evaluate their diagnostic accuracy for DM, DR, and R-DR diagnosis in all image types. Main Outcome Measures Area under the receiver operating characteristic curve (AUC) mean and standard deviation for each ML model and each individual and combined image types. Results A dataset of 726 eyes (439 individuals) were included. For DM diagnosis, the greatest AUC was observed for OCT (0.82, 0.03). For DR detection, the greatest AUC was observed for OCTA (0.77, 0.03), especially in the 3 × 3 mm superficial capillary plexus OCTA scan (0.76, 0.04). For R-DR diagnosis, the greatest AUC was observed for OCTA (0.87, 0.12) and the deep capillary plexus OCTA scan (0.86, 0.08). The addition of clinical variables (age, sex, etc.) improved most models AUC for DM, DR and R-DR diagnosis. The performance of the models was similar in unilateral and bilateral eyes image datasets. Conclusions Radiomics extracted from OCT and OCTA images allow identification of patients with DM, DR, and R-DR using standard ML classifiers. OCT was the best test for DM diagnosis, OCTA for DR and R-DR diagnosis and the addition of clinical variables improved most models. This pioneer study demonstrates that radiomics-based ML techniques applied to OCT and OCTA images may be an option for DR screening in patients with type 1 DM. Financial Disclosures Proprietary or commercial disclosure may be found after the references.
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Key Words
- AI, artificial intelligence
- AUC, area under the curve
- Artificial intelligence
- DCP, deep capillary plexus
- DM, diabetes mellitus
- DR, diabetic retinopathy
- Diabetic retinopathy
- FR, fundus retinographies
- LDA, linear discriminant analysis
- LR, logistic regression
- ML, machine learning
- Machine learning
- OCT angiography
- OCTA, OCT angiography
- R-DR, referable DR
- RF, random forest
- Radiomics
- SCP, superficial capillary plexus
- SVC, support vector classifier
- rbf, radial basis function
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Affiliation(s)
- Laura Carrera-Escalé
- Intelligent Data Science and Artificial Intelligence (IDEAI) Research Center,Department of Computer Science, Facultat d’Informàtica de Barcelona (FIB), Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Anass Benali
- Intelligent Data Science and Artificial Intelligence (IDEAI) Research Center,Department of Computer Science, Facultat d’Informàtica de Barcelona (FIB), Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Ann-Christin Rathert
- Intelligent Data Science and Artificial Intelligence (IDEAI) Research Center,Department of Computer Science, Facultat d’Informàtica de Barcelona (FIB), Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Ruben Martín-Pinardel
- Intelligent Data Science and Artificial Intelligence (IDEAI) Research Center,Department of Computer Science, Facultat d’Informàtica de Barcelona (FIB), Universitat Politècnica de Catalunya (UPC), Barcelona, Spain,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | | | - Anibal Alé-Chilet
- Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Marina Barraso
- Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sara Marín-Martinez
- Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Silvia Feu-Basilio
- Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Josep Rosinés-Fonoll
- Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Teresa Hernandez
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Irene Vilá
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Cristian Oliva
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Irene Vinagre
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Diabetes Unit, Hospital Clínic de Barcelona, Spain,Institut Clínic de Malalties Digestives i Metaboliques (ICMDM), Hospital Clínic de Barcelona, Spain
| | - Emilio Ortega
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Diabetes Unit, Hospital Clínic de Barcelona, Spain,Institut Clínic de Malalties Digestives i Metaboliques (ICMDM), Hospital Clínic de Barcelona, Spain
| | - Marga Gimenez
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Diabetes Unit, Hospital Clínic de Barcelona, Spain,Institut Clínic de Malalties Digestives i Metaboliques (ICMDM), Hospital Clínic de Barcelona, Spain
| | - Alfredo Vellido
- Intelligent Data Science and Artificial Intelligence (IDEAI) Research Center,Department of Computer Science, Facultat d’Informàtica de Barcelona (FIB), Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Enrique Romero
- Intelligent Data Science and Artificial Intelligence (IDEAI) Research Center,Department of Computer Science, Facultat d’Informàtica de Barcelona (FIB), Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Javier Zarranz-Ventura
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,Institut Clínic d´Oftalmología (ICOF), Hospital Clínic de Barcelona, Barcelona, Spain,Diabetes Unit, Hospital Clínic de Barcelona, Spain,School of Medicine, Universitat de Barcelona, Spain,Correspondence: Javier Zarranz-Ventura, MD, PhD, C/ Sabino Arana 1, Barcelona 08028, Spain.
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Wei J, Li R, Lu Y, Meng F, Xian B, Lai X, Lin X, Deng Y, Yang D, Zhang H, Li L, Ben X, Qiao G, Liu W, Li Z. Salivary microbiota may predict the presence of esophageal squamous cell carcinoma. Genes Dis 2022; 9:1143-1151. [PMID: 35685473 PMCID: PMC9170574 DOI: 10.1016/j.gendis.2021.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/25/2021] [Accepted: 02/09/2021] [Indexed: 01/11/2023] Open
Abstract
The aim is to explore the predictive value of salivary bacteria for the presence of esophageal squamous cell carcinoma (ESCC). Saliva samples were obtained from 178 patients with ESCC and 101 healthy controls, and allocated to screening and verification cohorts, respectively. In the screening phase, after saliva DNA was extracted, 16S rRNA V4 regions of salivary bacteria were amplified by polymerase chain reaction (PCR) with high-throughput sequencing. Highly expressed target bacteria were screened by Operational Taxonomic Units clustering, species annotation and microbial diversity assessment. In the verification phase, the expression levels of target bacteria identified in the screening phase were verified by absolute quantitative PCR (Q-PCR). Receiver operating characteristic (ROC) curves were plotted to investigate the predictive value of target salivary bacteria. LEfSe analysis revealed higher proportions of Fusobacterium, Streptococcus and Porphyromonas, and Q-PCR assay showed significantly higher numbers of Streptococcus salivarius, Fusobacterium nucleatum and Porphyromonas gingivalis in patients with ESCC, when compared with healthy controls (all P < 0.05). The areas under the ROC curves for Streptococcus salivarius, Fusobacterium nucleatum, Porphyromonas gingivalis and the combination of the three bacteria for predicting patients with ESCC were 69%, 56.5%, 61.8% and 76.4%, respectively. The sensitivities corresponding to cutoff value were 69.3%, 22.7%, 35.2% and 86.4%, respectively, and the matched specificity were 78.4%, 96.1%, 90.2% and 58.8%, respectively. These highly expressed Streptococcus salivarius, Fusobacterium nucleatum and Porphyromonas gingivalis in the saliva, alone or in combination, indicate their predictive value for ESCC.
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Affiliation(s)
- Junmin Wei
- Guangdong Provincial Institute of Geriatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Ruifeng Li
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China
- Wuhan No. 1 Hospital, Wuhan, Hubei 430022, PR China
| | - Yanxian Lu
- Guangdong Provincial Institute of Geriatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Fan Meng
- The First Affiliated Hospital, Gannan Medical University, Ganzhou, Jiangxi 341000, PR China
| | - Bohong Xian
- Guangdong Provincial Institute of Geriatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China
| | - Xiaorong Lai
- Medicine-Oncology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Xiayi Lin
- Concord Medical Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Yu Deng
- Concord Medical Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Dongyang Yang
- Medicine-Oncology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Huabin Zhang
- Concord Medical Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Liangfang Li
- Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Xiaosong Ben
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Wanwei Liu
- Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
| | - Zijun Li
- Guangdong Provincial Institute of Geriatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China
- Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, PR China
- Corresponding author. Department of Gastroenterology of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong Provincial Institute of Geriatrics, Concorde Medical Center, 106 Zhongshan Er Rd., Guangdong 510080, PR China. Fax: +008620 83826085.
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Gao FY, Chen HY, Luo YS, Chen JK, Yan L, Zhu JB, Fan GR, Zhou TT. "Q-markers targeted screening" strategy for comprehensive qualitative and quantitative analysis in fingerprints of Angelica dahurica with chemometric methods. Food Chem X 2021; 12:100162. [PMID: 34825171 PMCID: PMC8604777 DOI: 10.1016/j.fochx.2021.100162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/29/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022] Open
Abstract
Angelica dahurica is a famous functional food and herb. To guarantee quality of A. dahurica, a strategy “Q-markers targeted screening” was successfully developed by sufficient extraction of compounds and the targeted screening of qualitative and quantitative markers calculated through chemometric methods based fingerprints. Accelerated solvent extraction was selected due to its prominent advantages exhibiting the maximum extraction yields and varieties of compounds and especially excellent reproducibility (RSD < 1). After extraction, the fingerprints of A. dahuricae samples were established. For the preliminary herb authenticity, the targeted screening of 23 quantitative markers were performed by similarity analysis and hierarchical cluster analysis based on the fingerprints, which were identified by liquid chromatography tandem mass spectrometry (LC-MS). Subsequently, for further quality control, the targeted screening of nine quantitative markers were done by similarity analysis & linear discriminant analysis, which were determined by LC. Lastly, the strategy was successfully applied to quality assessment of A. dahurica samples.
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Key Words
- ANOVA, analysis of variance
- ASE, accelerated solvent extraction
- Accelerated solvent extraction
- Angelica dahurica
- BBD, Box-Bohnken Design
- CID, collision-induced-dissociation
- Chemometric analysis
- HCA, hierarchical cluster analysis
- HPLC-PDA-ESI-ITMSn, high performance liquid chromatography-photo diode array-electrospray ionization ion trap mass spectrometry
- HRE, heated reflux extraction
- IS, internal standard
- LDA, linear discriminant analysis
- LOD, limits of detection
- LOQ, limits of quantification
- Liquid chromatography tandem mass spectrometry
- MAE, microwave-assisted extraction
- Q-markers targeted screening
- Qualitative markers
- Quantitative markers
- RSD, relative standard deviation
- RSM, response surface methodology
- S/N, signal-to-noise ratios
- SA, similarity analysis
- TOF, time of fight
- UAME, ultrasonic-assisted microwave extraction
- UE, ultrasonic extraction
- UV, ultra violet
- bergapten (PubChem CID: 2355)
- estazolam (PubChem CID: 3261)
- hydrate oxypeucedanin (PubChem CID: 17536)
- imperatorin (PubChem CID: 10212)
- isoimperatorin (PubChem CID: 68081)
- oxypeucedanin (PubChem CID: 160544)
- phellopterin (PubChem CID: 98608)
- prangenin hydrate (PubChem CID: 129710912)
- xanthotoxin (PubChem CID: 4114)
- xanthotoxol (PubChem CID: 65090)
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Affiliation(s)
- Fang-Yuan Gao
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, No. 800 Xiangyin Road, Shanghai 200433, China
| | - Hai-Yan Chen
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, No. 415 Fengyang Road, Shanghai 200003, China
| | - Yu-Sha Luo
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, No. 325 Guohe Road, Shanghai 200433, China.,Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, No. 325 Guohe Road, Shanghai 200433, China
| | - Ji-Kuai Chen
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, No. 800 Xiangyin Road, Shanghai 200433, China
| | - Lang Yan
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, No. 800 Xiangyin Road, Shanghai 200433, China
| | - Jiang-Bo Zhu
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, No. 800 Xiangyin Road, Shanghai 200433, China
| | - Guo-Rong Fan
- Department of Clinical Pharmacy, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, No. 100 Haining Road, Shanghai 200025, China.,School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Ting-Ting Zhou
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, No. 325 Guohe Road, Shanghai 200433, China.,Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, No. 325 Guohe Road, Shanghai 200433, China
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4
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Mehta M, Naffa R, Zhang W, Schreurs NM, Waterland M, Cooper S, Holmes G. Validity and reliability of Raman spectroscopy for carotenoid assessment in cattle skin. Biochem Biophys Rep 2021; 27:101036. [PMID: 34141905 PMCID: PMC8188252 DOI: 10.1016/j.bbrep.2021.101036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022] Open
Abstract
Carotenoids are powerful antioxidants capable of helping to protect the skin from the damaging effects of exposure to sun by reducing the free radicals in skin produced by exposure to ultraviolet radiation, and they may also have a physical protective effect in human skin. Since carotenoids are lipophilic molecules which can be ingested with the diet, they can accumulate in significant quantities in the skin. Several studies on humans have been conducted to evaluate the protective function of carotenoids against various diseases, but there is very limited published information available to understand the mechanism of carotenoid bioavailability in animals. The current study was conducted to investigate the skin carotenoid level (SCL) in two cattle skin sets - weaners with an unknown feeding regime and New Generation Beef (NGB) cattle with monitored feed at three different ages. Rapid analytical and sensitive Raman spectroscopy has been shown to be of interest as a powerful technique for the detection of carotenoids in cattle skin due to the strong resonance enhancement with 532 nm laser excitation. The spectral difference of both types of skin were measured and quantified using univariate and linear discriminant analysis. SCL was higher in NGB cattle than weaners and there is a perfect classification accuracy between weaners and NGB cattle skin using carotenoid markers as a basis. Further work carried out on carotenoid rich NGB cattle skin of 8, 12 and 24 months of age identified an increasing trend in SCL with age. The present work validated the ability of Raman spectroscopy to determine the skin carotenoid level in cattle by comparing it with established HPLC methods. There is an excellent correlation of R2 = 0.96 between the two methods that could serve as a model for future application for larger population studies.
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Affiliation(s)
- Megha Mehta
- NZ Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Rafea Naffa
- NZ Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Wenkai Zhang
- NZ Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Nicola M. Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Mark Waterland
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Sue Cooper
- NZ Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Geoff Holmes
- NZ Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
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Zhao Z, Li F, Ning J, Peng R, Shang J, Liu H, Shang M, Bao XQ, Zhang D. Novel compound FLZ alleviates rotenone-induced PD mouse model by suppressing TLR4/MyD88/NF- κB pathway through microbiota-gut-brain axis. Acta Pharm Sin B 2021; 11:2859-2879. [PMID: 34589401 PMCID: PMC8463266 DOI: 10.1016/j.apsb.2021.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/07/2021] [Accepted: 02/12/2021] [Indexed: 01/09/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, but none of the current treatments for PD can halt the progress of the disease due to the limited understanding of the pathogenesis. In PD development, the communication between the brain and the gastrointestinal system influenced by gut microbiota is known as microbiota-gut-brain axis. However, the explicit mechanisms of microbiota dysbiosis in PD development have not been well elucidated yet. FLZ, a novel squamosamide derivative, has been proved to be effective in many PD models and is undergoing the phase I clinical trial to treat PD in China. Moreover, our previous pharmacokinetic study revealed that gut microbiota could regulate the absorption of FLZ in vivo. The aims of our study were to assess the protective effects of FLZ treatment on PD and to further explore the underlying microbiota-related mechanisms of PD by using FLZ as a tool. In the current study, chronic oral administration of rotenone was utilized to induce a mouse model to mimic the pathological process of PD. Here we revealed that FLZ treatment alleviated gastrointestinal dysfunctions, motor symptoms, and dopaminergic neuron death in rotenone-challenged mice. 16S rRNA sequencing found that PD-related microbiota alterations induced by rotenone were reversed by FLZ treatment. Remarkably, FLZ administration attenuated intestinal inflammation and gut barrier destruction, which subsequently inhibited systemic inflammation. Eventually, FLZ treatment restored blood-brain barrier structure and suppressed neuroinflammation by inhibiting the activation of astrocytes and microglia in the substantia nigra (SN). Further mechanistic research demonstrated that FLZ treatment suppressed the TLR4/MyD88/NF-κB pathway both in the SN and colon. Collectively, FLZ treatment ameliorates microbiota dysbiosis to protect the PD model via inhibiting TLR4 pathway, which contributes to one of the underlying mechanisms beneath its neuroprotective effects. Our research also supports the importance of microbiota-gut-brain axis in PD pathogenesis, suggesting its potential role as a novel therapeutic target for PD treatment.
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Key Words
- ANOSIM, adonis and analysis of similarity
- BBB, blood–brain barrier
- CFU, colony-forming units
- CMC-Na, sodium carboxymethyl cellulose
- CNS, central nerve system
- ELISA, enzyme-linked immunosorbent assay
- FD4, FITC-dextran (MW: 4 kDa)
- FITC, fluorescein isothiocyanate
- FLZ
- GFAP, glial fibrillary acidic protein
- GI, gastrointestinal
- Gastrointestinal dysfunction
- Hp, Helicobacter pylori
- IL-1β, interleukin-1β
- IL-6, interleukin-6
- Iba-1, ionized calcium-binding adapter molecule 1
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LBP, lipopolysaccharide binding protein
- LDA, linear discriminant analysis
- LPS, lipopolysaccharide
- MLNs, mesenteric lymph nodes
- Microbiota–gut–brain axis
- Neuroinflammation
- OTU, operational taxonomic unit
- PBS, phosphate-buffered saline
- PCoA, principal coordinate analysis
- PD, Parkinson's disease
- Parkinson's disease
- Rotenone mouse model
- SD, standard deviation
- SN, substantia nigra
- Systemic inflammation
- TEM, transmission electron microscopy
- TH, tyrosine hydroxylase
- TLR4, toll-like receptor 4
- TLR4/MyD88/NF-κB pathway
- TNF-α, tumor necrosis factor-α
- qPCR, quantitative polymerase chain reaction assay
- α-Syn, α-synuclein
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Affiliation(s)
- Zhe Zhao
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fangyuan Li
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jingwen Ning
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ran Peng
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Junmei Shang
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hui Liu
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Meiyu Shang
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiu-Qi Bao
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Dan Zhang
- State Key Laboratory of Bioactive Substrate and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Wahlang B, Alexander NC, Li X, Rouchka EC, Kirpich IA, Cave MC. Polychlorinated biphenyls altered gut microbiome in CAR and PXR knockout mice exhibiting toxicant-associated steatohepatitis. Toxicol Rep 2021; 8:536-547. [PMID: 33777700 PMCID: PMC7985695 DOI: 10.1016/j.toxrep.2021.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants associated with non-alcoholic fatty liver disease (NAFLD). Previously, we demonstrated that the PCB mixture, Aroclor1260, exacerbated NAFLD, reflective of toxicant-associated steatohepatitis, in diet-induced obese mice, in part through pregnane-xenobiotic receptor (PXR) and constitutive androstane receptor (CAR) activation. Recent studies have also reported PCB-induced changes in the gut microbiome that consequently impact NAFLD. Therefore, the objective of this study is to examine PCB effects on the gut-liver axis and characterize the role of CAR and PXR in microbiome alterations. C57Bl/6 (wildtype, WT), CAR and PXR knockout mice were fed a high fat diet and exposed to Aroclor1260 (20 mg/kg, oral gavage, 12 weeks). Metagenomics analysis of cecal samples revealed that CAR and/or PXR ablation increased bacterial alpha diversity regardless of exposure status. CAR and PXR ablation also increased bacterial composition (beta diversity) versus WT; Aroclor1260 altered beta diversity only in WT and CAR knockouts. Distinct changes in bacterial abundance at different taxonomic levels were observed between WT and knockout groups; however Aroclor1260 had modest effects on bacterial abundance within each genotype. Notably, both knockout groups displayed increased Actinobacteria and Verrucomicrobia abundance. In spite of improved bacterial diversity, the knockout groups however failed to show protection from PCB-induced hepato- and intestinal- toxicity including decreased mRNA levels of ileal permeability markers (occludin, claudin3). In summary, CAR and PXR ablation significantly altered gut microbiome in diet-induced obesity while Aroclor1260 compromised intestinal integrity in knockout mice, implicating interactions between PCBs and CAR, PXR on the gut-liver axis.
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Key Words
- ACHS, anniston community healthy survey
- AhR, arylhydrocarbon receptor
- Aroclor1260
- CAR, constitutive androstane receptor
- Camp, cathelicidin anti-microbial peptide
- Cdh5, adhesion molecule VE-cadherin
- Cldn, claudin
- Fasn, fatty acid synthase
- Fgf15, fibroblast growth factor 15
- Gut-liver
- HFD, high fat diet
- HOMA, homeostasis model assessment
- IBD, inflammatory bowel diseases
- LDA, linear discriminant analysis
- LEfSe, linear discriminant analysis effect size
- Microbiome
- Muc, mucin
- NAFLD
- NAFLD, nonalcoholic fatty liver disease
- NASH, nonalcoholic steatohepatitis
- OTU, operational taxonomic unit
- Ocln, occludin
- PCBs
- PCBs, polychlorinated biphenyls
- PXR, pregnane-xenobiotic receptor
- Pck1, phosphoenolpyruvate carboxykinase 1
- Ppara, peroxisome-proliferator activated receptor alpha
- RER, respiratory exchange rate
- Reg3g, regenerating islet-derived protein 3-gamma
- TASH
- TASH, toxicant-associated steatohepatitis
- Tff3, trefoil factor 3
- Tjp1, tight junction protein 1
- Tnfa, tumor necrosis factor
- WT, wildtype
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Affiliation(s)
- Banrida Wahlang
- UofL Superfund Research Center, University of Louisville, Louisville, KY, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | | | - Xiaohong Li
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY, USA
- KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, USA
| | - Eric C. Rouchka
- KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, USA
- Department of Computer Science and Engineering, J.B. Speed School of Engineering, University of Louisville, Louisville, KY, USA
| | - Irina A. Kirpich
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Matthew C. Cave
- UofL Superfund Research Center, University of Louisville, Louisville, KY, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
- Robley Rex Veterans Affairs Medical Center, Louisville, KY, USA
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7
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Parmanand B, Watson M, Boland KJ, Ramamurthy N, Wharton V, Morovat A, Lund EK, Collier J, Le Gall G, Kellingray L, Fairweather-Tait S, Cobbold JF, Narbad A, Ryan JD. Systemic iron reduction by venesection alters the gut microbiome in patients with haemochromatosis. JHEP Rep 2020; 2:100154. [PMID: 32995714 PMCID: PMC7516344 DOI: 10.1016/j.jhepr.2020.100154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/29/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
Background & Aims Iron reduction by venesection has been the cornerstone of treatment for haemochromatosis for decades, and its reported health benefits are many. Repeated phlebotomy can lead to a compensatory increase in intestinal iron absorption, reducing intestinal iron availability. Given that most gut bacteria are highly dependent on iron for survival, we postulated that, by reducing gut iron levels, venesection could alter the gut microbiota. Methods Clinical parameters, faecal bacterial composition and metabolomes were assessed before and during treatment in a group of patients with haemochromatosis undergoing iron reduction therapy. Results Systemic iron reduction was associated with an alteration of the gut microbiome, with changes evident in those who experienced reduced faecal iron availability with venesection. For example, levels of Faecalibacterium prausnitzii, a bacterium associated with improved colonic health, were increased in response to faecal iron reduction. Similarly, metabolomic changes were seen in association with reduced faecal iron levels. Conclusion These findings highlight a significant shift in the gut microbiome of patients who experience reduced colonic iron during venesection. Targeted depletion of faecal iron could represent a novel therapy for metabolic and inflammatory diseases, meriting further investigation. Lay summary Iron depletion by repeated venesection is the mainstay of treatment for haemochromatosis, an iron-overload disorder. Venesection has been associated with several health benefits, including improvements in liver function tests, reversal of liver scarring, and reduced risk of liver cancer. During iron depletion, iron absorption from the gastrointestinal (GI) tract increases to compensate for iron lost with treatment. Iron availability is limited in the GI tract and is crucial to the growth and function of many gut bacteria. In this study we show that reduced iron availability in the colon following venesection treatment leads to a change in the composition of the gut bacteria, a finding that, to date, has not been studied in patients with haemochromatosis. Venesection is the cornerstone of haemochromatosis treatment. Venesection leads to a compensatory increase in intestinal iron absorption. Reduced faecal iron availability leads to shifts in human colonic microbial composition. Changes in the human colonic metabolome occur with reduced faecal iron availability.
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Key Words
- ALT, alanine aminotransferase
- CRP, C-reactive protein
- FAAS, flame atomic absorption spectrophotometry
- GI, gastrointestinal
- HFE, hyperferritinaemia
- HH, hereditary haemachromatosis
- Haemochromatosis
- Iron
- LDA, linear discriminant analysis
- LEfSe, linear discriminant analysis effect size
- Microbiome
- TSP, 3-(trimethylsilyl)-propionate-d4
- Venesection
- WCC, white cell count
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Affiliation(s)
- Bhavika Parmanand
- Quadram Institute, Norwich, UK.,University of East Anglia, Norwich, UK
| | - Michael Watson
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Karen J Boland
- Department of Gastroenterology, Beaumont Hospital/Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Victoria Wharton
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Alireza Morovat
- Department of Clinical Biochemistry, Oxford University Hospitals Foundation Trust, Oxford, UK
| | | | - Jane Collier
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | | | | | - Jeremy F Cobbold
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - John D Ryan
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,Hepatology Unit, Beaumont Hospital/Royal College of Surgeons in Ireland, Dublin, Ireland
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Zhang X, Chen S, Duan F, Liu A, Li S, Zhong W, Sheng W, Chen J, Xu J, Xiao S. Prebiotics enhance the biotransformation and bioavailability of ginsenosides in rats by modulating gut microbiota. J Ginseng Res 2021; 45:334-43. [PMID: 33841014 DOI: 10.1016/j.jgr.2020.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 07/13/2020] [Accepted: 08/02/2020] [Indexed: 12/02/2022] Open
Abstract
Background Gut microbiota mainly function in the biotransformation of primary ginsenosides into bioactive metabolites. Herein, we investigated the effects of three prebiotic fibers by targeting gut microbiota on the metabolism of ginsenoside Rb1 in vivo. Methods Sprague Dawley rats were administered with ginsenoside Rb1 after a two-week prebiotic intervention of fructooligosaccharide, galactooligosaccharide, and fibersol-2, respectively. Pharmacokinetic analysis of ginsenoside Rb1 and its metabolites was performed, whilst the microbial composition and metabolic function of gut microbiota were examined by 16S rRNA gene amplicon and metagenomic shotgun sequencing. Results The results showed that peak plasma concentration and area under concentration time curve of ginsenoside Rb1 and its intermediate metabolites, ginsenoside Rd, F2, and compound K (CK), in the prebiotic intervention groups were increased at various degrees compared with those in the control group. Gut microbiota dramatically responded to the prebiotic treatment at both taxonomical and functional levels. The abundance of Prevotella, which possesses potential function to hydrolyze ginsenoside Rb1 into CK, was significantly elevated in the three prebiotic groups (P < 0.05). The gut metagenomic analysis also revealed the functional gene enrichment for terpenoid/polyketide metabolism, glycolysis, gluconeogenesis, propanoate metabolism, etc. Conclusion These findings imply that prebiotics may selectively promote the proliferation of certain bacterial stains with glycoside hydrolysis capacity, thereby, subsequently improving the biotransformation and bioavailability of primary ginsenosides in vivo.
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Key Words
- ANOVA, analysis of variance
- AUC, area under the concentration-time curve
- Bioavailability
- Biotransformation
- CAT, CAZymes Analysis Toolkit
- CAZymes, carbohydrate active enzymes
- CK, compound K
- Cmax, peak plasma concentration
- FDR, false discovery rate
- FOS, fructooligosaccharide
- GOS, galactooligosaccharide
- Ginsenoside
- Gut microbiota
- IS, internal standard
- KEGG, the Kyoto Encyclopaedia of Genes and Genomes
- LCA, lowest common ancestor
- LDA, linear discriminant analysis
- LEfSe, LDA effect size
- LLOQs, lower limits of quantifications
- MANOVA, multivariate ANOVA
- MRM, multiple reaction monitoring
- NMDS, non-metric multidimensional scaling
- PCA, principal component analysis
- PCoA, principal coordinates analysis
- Prebiotic
- SD, Sprague Dawley
- SRA, Sequence Read Archive
- Tmax, time of maximum plasma concentration
- UPLC-ESI-QqQ-MS/MS, ultra-high pressure liquid chromatography coupled to an electrospray ionization source and a triple-quadrupole mass spectrometer
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Peng J, Hao D, Yang L, Du M, Song X, Jiang H, Zhang Y, Zheng D. Evaluation of electrohysterogram measured from different gestational weeks for recognizing preterm delivery: a preliminary study using random Forest. Biocybern Biomed Eng 2020; 40:352-362. [PMID: 32308250 PMCID: PMC7153772 DOI: 10.1016/j.bbe.2019.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Developing a computational method for recognizing preterm delivery is important for timely diagnosis and treatment of preterm delivery. The main aim of this study was to evaluate electrohysterogram (EHG) signals recorded at different gestational weeks for recognizing the preterm delivery using random forest (RF). EHG signals from 300 pregnant women were divided into two groups depending on when the signals were recorded: i) preterm and term delivery with EHG recorded before the 26th week of gestation (denoted by PE and TE group), and ii) preterm and term delivery with EHG recorded during or after the 26th week of gestation (denoted by PL and TL group). 31 linear features and nonlinear features were derived from each EHG signal, and then compared comprehensively within PE and TE group, and PL and TL group. After employing the adaptive synthetic sampling approach and six-fold cross-validation, the accuracy (ACC), sensitivity, specificity and area under the curve (AUC) were applied to evaluate RF classification. For PL and TL group, RF achieved the ACC of 0.93, sensitivity of 0.89, specificity of 0.97, and AUC of 0.80. Similarly, their corresponding values were 0.92, 0.88, 0.96 and 0.88 for PE and TE group, indicating that RF could be used to recognize preterm delivery effectively with EHG signals recorded before the 26th week of gestation.
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Key Words
- ACC, accuracy
- ADASYN, adaptive synthetic sampling approach
- ANN, artificial neural network
- AR, auto-regressive model
- AUC, the area under the curve
- CorrDim, correlation dimension
- DT, decision tree
- EHG, electrohysterogram
- Electrohysterogram (EHG)
- Feature extraction
- Gestational week
- IUPC, intrauterine pressure catheter
- K-NN, K-nearest
- LDA, linear discriminant analysis
- LE, Lyapunov exponent
- MDF, median frequency
- MNF, mean frequency
- PE, preterm delivery before the 26th week of gestation
- PF, peak frequency
- PL, preterm delivery after the 26th week of gestation
- Preterm delivery
- QDA, quadratic discriminant analysis
- RF, random forest
- RMS, root mean square
- ROC, the receiver operating characteristic curve
- Random forest (RF).
- SD, standard deviation
- SE, energy values in signal
- SM, maximum values in signal
- SS, singular values in signal
- SV, variance values in signal
- SVM, support vector machine
- SampEn, sample entropy
- TE, term delivery before the 26th week of gestation
- TL, term delivery after the 26th week of gestation
- TOCO, tocodynamometer
- TPEHG, term-preterm electrohysterogram
- Tr, time reversibility
- τz, zero-crossing
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Affiliation(s)
- Jin Peng
- College of Life Science and Bioengineering, Beijing University of Technology, Intelligent Physiological Measurement and Clinical Translation, Beijing International Platform for Scientific and Technological Cooperation, Beijing, China
| | - Dongmei Hao
- College of Life Science and Bioengineering, Beijing University of Technology, Intelligent Physiological Measurement and Clinical Translation, Beijing International Platform for Scientific and Technological Cooperation, Beijing, China
| | - Lin Yang
- College of Life Science and Bioengineering, Beijing University of Technology, Intelligent Physiological Measurement and Clinical Translation, Beijing International Platform for Scientific and Technological Cooperation, Beijing, China
| | - Mengqing Du
- College of Life Science and Bioengineering, Beijing University of Technology, Intelligent Physiological Measurement and Clinical Translation, Beijing International Platform for Scientific and Technological Cooperation, Beijing, China
| | - Xiaoxiao Song
- College of Life Science and Bioengineering, Beijing University of Technology, Intelligent Physiological Measurement and Clinical Translation, Beijing International Platform for Scientific and Technological Cooperation, Beijing, China
| | - Hongqing Jiang
- Beijing Haidian Maternal and Children Health Hospital, Beijing, China
| | - Yunhan Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Intelligent Physiological Measurement and Clinical Translation, Beijing International Platform for Scientific and Technological Cooperation, Beijing, China
| | - Dingchang Zheng
- Centre for Intelligent Healthcare, Faculty of Health and Life Science, Coventry University, Coventry, UK
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10
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Cloete KJ, Šmit Ž, Minnis-Ndimba R, Vavpetič P, du Plessis A, le Roux SG, Pelicon P. Physico-elemental analysis of roasted organic coffee beans from Ethiopia, Colombia, Honduras, and Mexico using X-ray micro-computed tomography and external beam particle induced X-ray emission. Food Chem X 2019; 2:100032. [PMID: 31432016 PMCID: PMC6694858 DOI: 10.1016/j.fochx.2019.100032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 11/17/2022] Open
Abstract
The physico-elemental profiles of commercially attained and roasted organic coffee beans from Ethiopia, Colombia, Honduras, and Mexico were compared using light microscopy, X-ray micro-computed tomography, and external beam particle induced X-ray emission. External beam PIXE analysis detected P, S, Cl, K, Ca, Ti, Mn, Fe, Cu, Zn, Br, Rb, and Sr in samples. Linear discriminant analysis showed that there was no strong association between elemental data and production region, whilst a heatmap combined with hierarchical clustering showed that soil-plant physico-chemical properties may influence regional elemental signatures. Physical trait data showed that Mexican coffee beans weighed significantly more than beans from other regions, whilst Honduras beans had the highest width. X-ray micro-computed tomography qualitative data showed heterogeneous microstructural features within and between beans representing different regions. In conclusion, such multi-dimensional analysis may present a promising tool in assessing the nutritional content and qualitative characteristics of food products such as coffee.
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Affiliation(s)
- Karen J. Cloete
- iThemba Laboratory for Accelerator Based Sciences, National Research Foundation, PO Box 722, Somerset West 7129, South Africa
| | - Žiga Šmit
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica, 19, SI-1000 Ljubljana, Slovenia
| | - Roya Minnis-Ndimba
- iThemba Laboratory for Accelerator Based Sciences, National Research Foundation, PO Box 722, Somerset West 7129, South Africa
| | - Primož Vavpetič
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
| | - Anton du Plessis
- CT Scanner Facility, Central Analytical Facilities, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Stephan G. le Roux
- CT Scanner Facility, Central Analytical Facilities, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Primož Pelicon
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
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11
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Ambure P, Bhat J, Puzyn T, Roy K. Identifying natural compounds as multi-target-directed ligands against Alzheimer's disease: an in silico approach. J Biomol Struct Dyn 2018; 37:1282-1306. [PMID: 29578387 DOI: 10.1080/07391102.2018.1456975] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Alzheimer's disease (AD) is a multi-factorial disease, which can be simply outlined as an irreversible and progressive neurodegenerative disorder with an unclear root cause. It is a major cause of dementia in old aged people. In the present study, utilizing the structural and biological activity information of ligands for five important and mostly studied vital targets (i.e. cyclin-dependant kinase 5, β-secretase, monoamine oxidase B, glycogen synthase kinase 3β, acetylcholinesterase) that are believed to be effective against AD, we have developed five classification models using linear discriminant analysis (LDA) technique. Considering the importance of data curation, we have given more attention towards the chemical and biological data curation, which is a difficult task especially in case of big data-sets. Thus, to ease the curation process we have designed Konstanz Information Miner (KNIME) workflows, which are made available at http://teqip.jdvu.ac.in/QSAR_Tools/ . The developed models were appropriately validated based on the predictions for experiment derived data from test sets, as well as true external set compounds including known multi-target compounds. The domain of applicability for each classification model was checked based on a confidence estimation approach. Further, these validated models were employed for screening of natural compounds collected from the InterBioScreen natural database ( https://www.ibscreen.com/natural-compounds ). Further, the natural compounds that were categorized as 'actives' in at least two classification models out of five developed models were considered as multi-target leads, and these compounds were further screened using the drug-like filter, molecular docking technique and then thoroughly analyzed using molecular dynamics studies. Finally, the most potential multi-target natural compounds against AD are suggested.
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Key Words
- 3D, three-dimensional
- ACh, acetylcholine
- AChE, acetylcholinesterase
- AD, Alzheimer’s disease
- ADME, absorption, distribution, metabolism, and elimination
- APP, amyloid precursor protein
- AUROC, area under the ROC curve
- Alzheimer’s disease
- Aβ, amyloid beta
- BACE1, beta-APP-cleaving enzyme 1
- CDK5, cyclin-dependant kinase 5
- FDA, food and drug administration
- FN, false negative
- FP, false positive
- GSK-3β, glycogen synthase kinase 3β
- HTVS, high-throughput virtual screening
- InChI, International Chemical Identifier
- KNIME, Konstanz Information Miner
- LBDD, ligand-based drug design
- LDA, linear discriminant analysis
- MAO-B, monoamine oxidase B
- MMGBSA, molecular mechanics/generalized born surface area
- MMPBSA, molecular mechanics/Poisson–Boltzmann surface area
- MMPs, matched molecular pairs
- MSA, molecular spectrum analysis
- MTDLs, multi-target-directed ligands
- NMDA, N-methyl-D-aspartate
- PDB, protein data bank
- PP, posterior probability
- QSAR, quantitative structure–activity relationship
- RMSD, root-mean-square deviation
- ROC, receiver operating curve
- ROS, reactive oxygen species
- SBDD, structure-based drug design
- SDF, structure data format
- SMILES, simplified molecular-input line-entry system
- TN, true negative
- TP, true positive
- big data
- data curation
- linear discriminant analysis
- molecular docking
- molecular dynamics
- multi-target drug design
- natural compounds
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Affiliation(s)
- Pravin Ambure
- a Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology , Jadavpur University , Kolkata 700 032 , India
| | - Jyotsna Bhat
- b Laboratory of Environmental Chemometrics, Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63, Gdańsk 80-308 , Poland
| | - Tomasz Puzyn
- b Laboratory of Environmental Chemometrics, Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63, Gdańsk 80-308 , Poland
| | - Kunal Roy
- a Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology , Jadavpur University , Kolkata 700 032 , India
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12
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Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V. Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease. Cell Mol Gastroenterol Hepatol 2016; 2:563-566.e5. [PMID: 28174737 PMCID: PMC5042890 DOI: 10.1016/j.jcmgh.2016.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/15/2016] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer. Diseased and healthy-appearing ileum was identified using microscopy, and paraffin blocks were macrodissected using a core needle to specifically isolate DNA. Illumina Whole Genome Sequencing was used for microbial sequence identification and subsequent taxonomic classification using the PathSeq tool. RESULTS We observed significant differences between the microbiome of CD samples vs inflammatory bowel disease-free controls, including depletion of Bacteroidetes and Clostridia. Notably, microbial composition at the phyla level did not differ markedly between healthy and diseased areas of CD patients. However, we observed enrichment of potentially pathogenic organisms at the species level. CONCLUSIONS Our study showed dysbiosis within deeper layers of the ileum of CD patients, specifically enrichment of enterotoxigenic Staphylococcus aureus and an environmental Mycobacterium species not described previously. Future studies with larger cohort sizes are warranted to confirm these findings. Studies would benefit from effective microbial DNA extraction methods from paraffin sections and host nucleic acid depletion approaches to increase microbial read coverage.
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Affiliation(s)
- Chandra Sekhar Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Ami S. Bhatt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sharyle Fowler
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Jacqueline Durand
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Joonil Jung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Fujiko Duke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Veronica Manzo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Diana Cai
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Akinyemi I. Ojesina
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aruna Ramachandran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ramnik J. Xavier
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Atul K. Bhan
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts,Matthew Meyerson, MD, PhD, Dana-Farber Cancer Institute, Boston, Massachusetts 02215. fax: 617-582-7880.Dana-Farber Cancer InstituteBostonMassachusetts 02215
| | - Vijay Yajnik
- Crohn’s and Colitis Center, Massachusetts General Hospital, Boston, Massachusetts,Correspondence Address correspondence to: Vijay Yajnik, MD, PhD, Crohn's and Colitis Center, Massachusetts General Hospital, Massachusetts 02114.Crohn's and Colitis CenterMassachusetts General HospitalMassachusetts 02114
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13
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Irimia A, Wang B, Aylward SR, Prastawa MW, Pace DF, Gerig G, Hovda DA, Kikinis R, Vespa PM, Van Horn JD. Neuroimaging of structural pathology and connectomics in traumatic brain injury: Toward personalized outcome prediction. Neuroimage Clin 2012; 1:1-17. [PMID: 24179732 PMCID: PMC3757727 DOI: 10.1016/j.nicl.2012.08.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 11/01/2022]
Abstract
Recent contributions to the body of knowledge on traumatic brain injury (TBI) favor the view that multimodal neuroimaging using structural and functional magnetic resonance imaging (MRI and fMRI, respectively) as well as diffusion tensor imaging (DTI) has excellent potential to identify novel biomarkers and predictors of TBI outcome. This is particularly the case when such methods are appropriately combined with volumetric/morphometric analysis of brain structures and with the exploration of TBI-related changes in brain network properties at the level of the connectome. In this context, our present review summarizes recent developments on the roles of these two techniques in the search for novel structural neuroimaging biomarkers that have TBI outcome prognostication value. The themes being explored cover notable trends in this area of research, including (1) the role of advanced MRI processing methods in the analysis of structural pathology, (2) the use of brain connectomics and network analysis to identify outcome biomarkers, and (3) the application of multivariate statistics to predict outcome using neuroimaging metrics. The goal of the review is to draw the community's attention to these recent advances on TBI outcome prediction methods and to encourage the development of new methodologies whereby structural neuroimaging can be used to identify biomarkers of TBI outcome.
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Key Words
- 3D, three-dimensional
- AAL, Automatic Anatomical Labeling
- ADC, apparent diffusion coefficient
- ANTS, Advanced Normalization ToolS
- BOLD, blood oxygen level dependent
- CC, corpus callosum
- CT, computed tomography
- DAI, diffuse axonal injury
- DSI, diffusion spectrum imaging
- DTI, diffusion tensor imaging
- DWI, diffusion weighted imaging
- Diffusion tensor
- FA, fractional anisotropy
- FLAIR, Fluid Attenuated Inversion Recovery
- FSE, Functional Status Examination
- GCS, Glasgow Coma Score
- GM, gray matter
- GOS, Glasgow Outcome Score
- GRE, Gradient Recalled Echo
- HARDI, high-angular-resolution diffusion imaging
- IBA, Individual Brain Atlas
- LDA, linear discriminant analysis
- MRI, magnetic resonance imaging
- MRI/fMRI
- NINDS, National Institute of Neurological Disorders and Stroke
- Neuroimaging
- Outcome measures
- PCA, principal component analysis
- PROMO, PROspective MOtion Correction
- SPM, Statistical Parametric Mapping
- SWI, Susceptibility Weighted Imaging
- TBI, traumatic brain injury
- TBSS, tract-based spatial statistics
- Trauma
- WM, white matter
- fMRI, functional magnetic resonance imaging
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Affiliation(s)
- Andrei Irimia
- Laboratory of Neuro Imaging, Department of Neurology, University of California, Los Angeles, CA 90095, USA
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