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Proteomics techniques in protein biomarker discovery

Quantitative Biology 2024年第1期12卷 53-69页

作者： mahsa babaei Soheila Kashanian Huang-Teck Lee Frances Harding Department of Biology Faculty of ScienceRazi UniversityKermanshahIran Faculty of Chemistry Sensor and Biosensor Research Center(SBRC)Razi UniversityKermanshahIran Nanobiotechnology Department Faculty of Innovative Science and TechnologyRazi UniversityKermanshahIran Centre for Marine Bioproducts Development Flinders UniversityAdelaideSouth AustraliaAustralia Monash Institute of Pharmaceutical Sciences Monash UniversityMelbourneNew South WalesAustralia

Protein biomarkers represent specific biological activities and processes, so they have had a critical role in cancer diagnosis and medical care for more than 50 years. With the recent improvement in proteomics technologies, thousands of protein biomarker candidates have been developed for diverse disease states. Studies have used different types of samples for proteomics diagnosis. Samples were pretreated with appropriate techniques to increase the selectivity and sensitivity of the downstream analysis and purified to remove the contaminants. The purified samples were analyzed by several principal proteomics techniques to identify the specific protein. In this study, recent improvements in protein biomarker discovery, verification, and validation are investigated. Furthermore, the advantages, and disadvantages of conventional techniques, are discussed. Studies have used mass spectroscopy (MS) as a critical technique in the identification and quantification of candidate biomarkers. Nevertheless, after protein biomarker discovery, verification and validation have been required to reduce the false-positive rate where there have been higher number of samples. Multiple reaction monitoring (MRM), parallel reaction monitoring (PRM), and selected reaction monitoring (SRM), in combination with stable isotope-labeled internal standards, have been examined as options for biomarker verification, and enzyme-linked immunosorbent assay (ELISA) for validation.

关键词： biomarker discovery cancer biomarker gel-based methods gel-free methods mass spectroscopy proteomics

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Examining the Effect of Hydroalcoholic Extract of Dracaena cinnabari on Sex Hormones and Ovarian and Uterine Tissues of Rats

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World Journal of Traditional Chinese Medicine 2024年第2期10卷 213-219页

作者： Elham Najafi Bahareh babaei Hoolari Akbar Karimi Aliasghar Pilehvarian Department of Cellular Biology Genesis Evolution-Develoment Isfahan Payame Noor University Department of Anatomy School of Medicine Tehran University of Medical Sciences Department of Biology Group Faculty Member of Isfahan Payame Noor University

Introduction: Dracaena cinnabari is considered a rich source of phytochemicals used widely in traditional medicine. In the present study, the effect of D. cinnabari hydraulic extract on the reproductive system of female rats was investigated. Methods: The samples were randomly divided into four groups(six samples in each group), including three treatment groups and one control group, and all samples were kept at the same conditions. Hydraulic extract of D. cinnabari and injected intraperitoneally daily for 10 days, while physiological serum was used for injection in to the control group. After 10 days of injection, estrogen and progesterone levels were measured by enzyme immunoassay technique. After dissection, the ovaries and uterine tissues were isolated for histological examination, and tissue changes were carefully examined. Results: The results revealed that the levels of estrogen and progesterone in experimental Groups 2 and 3 had a significant increase(P < 0.001). Regarding tissue changes, a significant increase was observed in epithelial thickness(P < 0.001), number of corpus luteum(P < 0.01), and Graafian follicle(P < 0.01) in doses of 100 and 150 mg/kg. Conclusions: Based on the results, it seems that D. cinnabari extract has an effect on the ovarian follicles.

关键词： Dracaena cinnabari herbal medicine ovarian tissues reproductive sex hormones

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Exercise training modulates adipokine dysregulations in metabolic syndrome

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Sports Medicine and Health Science 2022年第1期4卷 18-28页

作者： Parvin babaei Rastegar Hoseini Cellular&Molecular Research Center School of MedicineGuilan University of Medical SciencesRashtIran Neuroscience Research Center School of MedicineGuilan University of Medical SciencesRashtIran Department of Physiology School of MedicineGuilan University of Medical SciencesRashtIran Department of Sports Physiology Faculty of Sport SciencesRazi UniversityKermanshahIran

Metabolic syndrome(MetS)is a cluster of risk factors for various metabolic diseases,and it is characterized by central obesity,dyslipidemia,hypertension,and insulin resistance.The core component for MetS is adipose tissue,which releases adipokines and influences physical health.Adipokines consist of pro and anti-inflammatory cytokines and contribute to various physiological functions.Generally,a sedentary lifestyle promotes fat accumulation and secretion of pro-inflammatory adipokines.However,regular exercise has been known to exert various beneficial effects on metabolic and cognitive disorders.Although the mechanisms underlying exercise beneficial effects in MetS are not fully understood,changes in energy expenditure,fat accumulation,circulatory level of myokines,and adipokines might be involved.This review article focuses on some of the selected adipokines in MetS,and their responses to exercise training considering possible mechanisms.

关键词： Adipokines Insulin resistance Aerobic training Resistance training Metabolic syndrome

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Impressive strides in amelioration of corrosion and wear behaviors of Mg alloys using applied polymer coatings on PEO porous coatings:A review

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Journal of Magnesium and Alloys 2022年第5期10卷 1171-1190页

作者： Arash Fattah-alhosseini Razieh Chaharmahali Kazem babaei Department of Materials Engineering Bu-Ali Sina UniversityHamedan 65178-38695Iran

Magnesium(Mg)and its alloys have received much attention in a lot of areas due to their special chemical and physical properties.Nevertheless,high corrosion rates are a limiting factor.The plasma electrolytic oxidation(PEO)technique is a simple approach to place an oxide film on the surface of light metals like Mg alloys.This method has been considered for controlling the rate of corrosion and improving some other properties.On the other hand,PEO coatings cannot make enough protection of Magnesium alloys for a long time due to porosity and fine cracks.Therefore,PEO-based composite coatings are used to make adequate corrosion protection on the Mg alloys surface.The popularity of these coatings is due to their good corrosion resistance,simplicity,high coating capability,and cost-effectiveness in complex segments.Formation of an organic layer on the surface of PEO coating is one of the effective methods to close the defects and thus prevent the corrosive species penetration into the substrate.Coating the PEO coating with a polymer layer can be a good solution to control the amount of damage and improve the corrosion and abrasion resistance.In addition,PEO coating can eliminate the problems of insufficient adhesion of polymer coatings and is considered as a suitable base for composite coatings.This review paper presents the corrosion and abrasion behavior of the PEO/Polymer dual coating system on Mg alloys.Given the fundamental role of coatings thickness and morphology in wear and corrosion behavior,these aspects have been highly discussed in this study.

关键词： Composite coating Mg alloys PEO Polymer Corrosion properties Wear resistance

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Antibacterial activity of bioceramic coatings on Mg and its alloys created by plasma electrolytic oxidation(PEO): A review

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Journal of Magnesium and Alloys 2022年第1期10卷 88-106页

作者： Arash Fattah-alhosseini Maryam Molaei Meisam Nouri Kazem babaei Department of Materials Engineering Bu-Ali Sina UniversityHamedan 65178-38695Iran

Mg and its alloys are suitable choices for implant materials due to their biodegradability and biocompatibility features. However, the high electrochemical activity of this family of biomaterials results in their fast degradation and severe corrosion in the physiological environment,producing hydrogen(H;) gas, and therefore increasing the p H of the environment. To meet the clinical requirements, the degradation rate of Mg biomaterials needs to be reduced. Nevertheless, higher corrosion resistance of Mg results in a low alkaline p H, weakening the antibacterial activity. Therefore, while the rapid degradation problem of Mg-based biomaterials needs to be addressed, good antibacterial properties are also necessary. By using the plasma electrolytic oxidation(PEO) surface modification technique, the antibacterial activity of Mg and its alloys can be enhanced while maintaining their corrosion protection properties at a high level. Throughout the PEO process, introducing antibacterial agents into solutions results in a major increase in antibacterial activity of the coatings. Moreover, post-or pre-processing on PEO coatings can provide better protection against bacteria. In this review, the antibacterial activity of PEO coatings applied on Mg and also its alloys will be discussed in more detail.

关键词： Antibacterial activity Magnesium Plasma electrolytic oxidation(PEO) Gram-positive bacteria Gram-negative bacteria

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Cell therapy for the treatment of reproductive diseases and infertility:an overview from the mechanism to the clinic alongside diagnostic methods

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Frontiers of Medicine 2022年第6期16卷 827-858页

作者： Kosar babaei Mohsen Aziminezhad Seyedeh Elham Norollahi Sogand Vahidi Ali Akbar Samadani Non-Communicable Disease Research Center Neyshabur University of Medical SciencesNeyshaburIran UMR INSERM U 1122 IGE-PCVInteractions Gène-Environment En Physiopathologie Cardiovascular UniversitéDe LorraineNancyFrance Cancer Research Center and Department of Immunology Semnan University of Medical SciencesSemnanIran Medical Biology Research Center Kermanshah University of Medical SciencesKermanshahIran Guilan Road Trauma Research Center Guilan University of Medical SciencesRashtIran

Infertility is experienced by 8%–12%of adults in their reproductive period globally and has become a prevalent concern.Besides routine therapeutic methods,stem cells are rapidly being examined as viable alternative therapies in regenerative medicine and translational investigation.Remarkable progress has been made in understanding the biology and purpose of stem cells.The affected pluripotent stem cells(iPSCs)and mesenchymal stem cells(MSCs)are further studied for their possible use in reproductive medicine,particularly for infertility induced by premature ovarian insufficiency and azoospermia.Accordingly,this study discusses current developments in the use of some kinds of MSCs such as adipose-derived stem cells,bone marrow stromal cells,umbilical cord MSCs,and menstrual blood MSCs.These methods have been used to manage ovarian and uterine disorders,and each technique presents a novel method for the therapy of infertility.

关键词： infertility stem cell therapy mesenchymal stem cells pluripotent stem cells

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Dielectric spectroscopy coupled with artificial neural network for classification and quantification of sesame oil adulteration

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Information Processing in Agriculture 2022年第2期9卷 233-242页

作者： Mahmoud Soltani Firouz Mahmoud Omid Mehrdad babaei Mahdi Rashvand Department of Agricultural Machinery Engineering Faculty of Agricultural Engineering and TechnologyUniversity of TehranKarajIran Machine Design and Mechatronics Department Institute of MechanicsIranian Research Organization for Science and TechnologyTehranIran

Adulteration using cheap vegetable oils into expensive oils such as sesame oil is a considerable challenge in the edible oil market. To discriminate pure and adulterated sesame oilwith sunflower and canola oils (commonly used as an adulterant to the high-price oils),dielectric spectroscopy was applied in the range of 40 kHz–20 MHz. The principal component analysis (PCA) plots were able to distinguish the pure sesame oil, while it was impossible to separate the adulterated oils based on the kind of adulteration. The correlationbased feature selection (CFS) method was used to select the more relevant dielectric datawithin the spectrum and to reduce the dimensionality of the input vector belongs to theartificial neural network (ANN). The ANN classifier with topology of 19-5-4 structureshowed a perfect accuracy of 100% in detecting the authentic and the adulterated sesameoil. The regression ANN with the topology of 15-5-1, 21-8-1 and 10-11-1 were the mostrobust models in quantifying the amount of adulteration in sesame oil generated by sun-flower oil, canola oil and sunflower + canola oils, with R2Test of 1, 1 and 0.999 9, respectively.The proposed technique is a powerful and simple method to detect and quantify adulteration of sesame oil. The novelty of this research is capability of used system for authentication of adulterated sesame oil using low frequency. Furthermore, the developed systemhas a good capability for other types of sesame oil adulterations as well as to detect adulteration in other expensive edible oils.

关键词： Adulteration Artificial neural network Chemometrics Sesame oil Correlation-based feature selection Principal component analysis

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A review of effective strides in amelioration of the biocompatibility of PEO coatings on Mg alloys

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Journal of Magnesium and Alloys 2022年第9期10卷 2354-2383页

作者： Arash Fattah-alhosseini Razieh Chaharmahali Kazem babaei Meisam Nouri Mohsen K.Keshavarz Mosab Kaseem Department of Materials Engineering Bu-Ali Sina UniversityHamedan 65178-38695Iran Department of Mechanical and Mechatronics Engineering University of WaterlooWaterlooON N2L 3G1Canada Department of Nanotechnology and Advanced Materials Engineering Sejong UniversitySeoul 05006Republic of Korea

Recently,developing bioactive and biocompatible materials based on Mg and Mg-alloys for implant applications has drawn attention among researchers owing to their suitable body degradability.Implementing Mg and its alloys reduces the risk of long-term incompatibility with tissues because of their close mechanical properties and no need for re-operation to remove the implant.Nevertheless,the degradation rate of the implant needs to be controlled because production of hydrogen gas and accumulation of its bubbles increases local pH around the implants.To confine the integrity of implants and the body,the corrosion concern in the body fluid requires to be addressed.Surface modification as one of the effective strategies can improve corrosion resistance.Besides,it creates a suitable surface for bone grafting and cell growth.The development of proper surface-coated implants needs appropriate techniques and approaches.Plasma electrolytic oxidation(PEO)coating can provide long-term protection by providing a ceramic layer and improving the implant’s biocompatibility.Herein,a general review of in-vivo and in-vitro evaluation of PEO coatings on Mg and Mg-alloys has been carried out.Recent advances in surface modification on Mg and Mg-alloys have been discussed,however,the need for reliable laboratory models to predict in-vivo degradation is still valid.

关键词： Mg alloys Biodegradation Surface modification In-vivo In-vitro PEO coatings

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Hyaluronic acid algorithm-based models for assessment of liver fibrosis： translation from basic science to clinical application

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Hepatobiliary & Pancreatic Diseases International 2016年第2期15卷 131-140页

作者： Zeinab babaei Hadi Parsian Student Research Committee&Department of Biochemistry and Biophysics Babol University of Medical SciencesBabolIran Cellular and Molecular Biology Research Center Health Research InstituteBabol University of Medical SciencesBabolIran

BACKGROUND： The estimation of liver fibrosis is usually dependent on liver biopsy evaluation. Because of its disadvantages and side effects, researchers try to find non-invasive methods for the assessment of liver injuries. Hyaluronic acid has been proposed as an index for scoring the severity of fibrosis, alone or in algorithm models. The algorithm model in which hyaluronic acid was used as a major constituent was more reliable and accurate in diagnosis than hyaluronic acid alone. This review described various hyaluronic acid algorithm-based models for assessing liver fibrosis.DATA SOURCE： A Pub Med database search was performed to identify the articles relevant to hyaluronic acid algorithmbased models for estimating liver fibrosis.RESULT： The use of hyaluronic acid in an algorithm model is an extra and valuable tool for assessing liver fibrosis.CONCLUSIONS： Although hyaluronic acid algorithm-based models have good diagnostic power in liver fibrosis assessment, they cannot render the need for liver biopsy obsolete and it is better to use them in parallel with liver biopsy. They can be used when frequent liver biopsy is not possible in situations such as highlighting the efficacy of treatment protocol for liver fibrosis.

关键词： algorithm hyaluronic acid liver disease liver fibrosis

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Kaempferol attenuates cognitive deficit via regulating oxidative stress and neuroinflammation in an ovariectomized rat model of sporadic dementia

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Neural Regeneration Research 2018年第10期13卷 1827-1832页

作者： Somayeh Kouhestani Adele Jafari Parvin babaei Cellular and Molecular Research Center Faculty of MedicineGuilan University of Medical Sciences Department of Physiology Faculty of MedicineGuilan University of Medical Sciences Neuroscience Research Center Guilan University of Medical Sciences

Alzheimer＇s disease（AD） is associated with oxidative stress, and ultimately results in cognitive deficit. Despite existing literature on the pathophysiology of AD, there is currently no cure for AD. The present study investigated the effects of kaempferol（Kmp） isolated from the extract of Mespilus germanica L.（medlar） leaves on cognitive impairment, hippocampal antioxidants, apoptosis, lipid peroxidation and neuro-inflammation markers in ovariectomized（OVX） rat models of sporadic AD. Kaempferol, as the main flavonoid of medlar extract has been previously known for anti-oxidative, anti-inflammatory and anti-neurotoxic effects. Thirty-two female Wistar rats were ovariectomized, and randomly divided into four groups： sham, OVX ＋ saline, OVX ＋ streptozotocin（STZ）＋ saline, OVX ＋ STZ ＋ Kmp. Animals received intracerebroventricular injection of STZ（3 mg/kg, twice with one day interval） to establish models of sporadic AD. Intraperitoneal injection of Kmp（10 mg/kg） for 21 days was performed in the OVX ＋ STZ ＋ Kmp group. Spatial learning and memory of rats were evaluated using a Morris water maze. Finally, brain homogenates were used for biochemical analysis by enzyme-linked immunosorbent assay. The results showed a significant improvement in spatial learning and memory as evidenced by shortened escape latency and searching distance in Morris water maze in the OVX ＋ STZ ＋ Kmp group compared with the OVX ＋ STZ group. Kmp also exhibited significant elevations in brain levels of antioxidant enzymes of superoxide dismutase and glutathione, while reduction in tumor necrosis factor-α and malondialdehyde. Our results demonstrate that Kmp is capable of alleviating STZ-induced memory impairment in OVX rats, probably by elevating endogenous hippocampal antioxidants of superoxide dismutase and glutathione, and reducing neuroinflammation. This study suggests that Kmp may be a potential neuroprotective agent against cognitive deficit in AD.

关键词： Alzheimer＇s disease oxidative stress neuroinflammation Mespilus germanica L. Kaempferol neural regeneration

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