1.Mass Spectrometry-based Antibody Sequencing Technologies
Sheng-Mei LIU ; Peng XUE ; Xiao-Jian WANG
Progress in Biochemistry and Biophysics 2026;53(4):840-854
Antibodies play a critical role in adaptive immune responses and serve as key components in disease diagnosis and treatment. These molecules exhibit dynamic post-translational modifications (PTMs), such as glycosylation and phosphorylation, which regulate their effector functions. To date, nearly all of our knowledge about antibody repertoires has come from B cell receptor (BCR) sequencing (BCR-seq), which facilitates the profiling of clonal composition and the tracing of maturation trajectories within B-cell repertoires. However, circulating antibodies found in bodily fluids—such as serum, saliva, milk, mucosal secretions, and cerebrospinal fluid—exhibit diversities and specificities beyond what BCR-seq alone can predict. Therefore, identifying and quantifying antibody clonotypes at the protein level could enhance diagnosis, prognosis, and treatment strategies in personalized medicine. The critical gap between genotype and phenotype necessitates complementary methodologies that enable the direct characterization of antibody proteins in their native functional states. Mass spectrometry (MS)-based antibody repertoire sequencing (Ab-seq) is currently the only feasible approach for this task and primarily includes database-dependent methods—such as bottom-up, middle-down, and top-down approaches—as well as database-independent de novo sequencing technology. These strategies enable multi-level, high-precision characterization ranging from peptides and domains to intact antibody molecules. Unlike the shotgun strategy commonly used in routine proteomics, obtaining full sequences of all antibodies presents unique challenges. It requires specialized methodological adaptations to address issues related to dynamic range, sequence variation, and sample complexity. This review introduces the technical principles, methodological workflows, and recent applications of various mass spectrometry-based antibody repertoire sequencing (Ab-seq) strategies, with a focus on approaches designed to improve sequence coverage and identification accuracy. These include multi-enzyme digestion, hybrid fragmentation methods, and artificial intelligence-assisted de novo sequencing. By systematically comparing database-dependent techniques—such as bottom-up, middle-down, and top-down approaches—with database-independent de novo sequencing, this review outlines their respective advantages and limitations in terms of sample throughput, sequence coverage, post-translational modification characterization, and data analysis complexity. In addition, this review discusses emerging technological trends, including the integration of ion mobility separation, native mass spectrometry, and artificial intelligence-driven data interpretation, which are expected to enhance the depth and accuracy of antibody characterization. Although current methods continue to face challenges related to sample complexity, dynamic range, and unambiguous sequence variant assignment, we emphasize the importance of integrating BCR-seq and Ab-seq data to construct gene-protein association maps. These maps help validate sequence accuracy and facilitate epitope discovery. This dual-platform strategy helps bridge the gap between genotype and phenotype, thereby enhancing both the resolution and scope of antibody repertoire studies. Such an integrative approach also offers a valuable tool for therapeutic antibody development, structure-function analysis, and precise evaluation of vaccine efficacy.
2.Olfactory Receptors Expressed in The Intestine and Their Functions
Pei-Wen YANG ; Meng-Meng YUAN ; Ying ZHOU ; Peng LI ; Gui-Hong QI ; Ying YANG ; Zhong-Yi MAO ; Meng-Sha ZHOU ; Xiao-Shuang MAO ; Jian-Ping XIE ; Yi-Nan YANG ; Shi-Hao SUN
Progress in Biochemistry and Biophysics 2026;53(3):534-549
Olfactory receptors (ORs) form the largest superfamily of G protein-coupled receptors (GPCRs). Traditionally recognized for their role in the nasal olfactory epithelium, where they mediate the sense of smell, accumulating evidence has firmly established their ectopic expression in non-olfactory tissues, including the intestine, lungs, and kidneys. The intestine, as the primary site for nutrient digestion and absorption, harbors a highly complex chemical environment. To adapt to this environment, the gut employs a sophisticated network of “chemosensors” to monitor luminal contents and maintain homeostasis. Among these sensors, intestinal ORs have emerged as crucial functional components, serving as a molecular bridge that connects environmental chemical signals—such as food-derived odorants—to specific physiological responses. This discovery has significantly deepened our understanding of how dietary flavors and compounds influence intestinal physiology at the molecular level. This review systematically summarizes the expression profiles, ligand classification, and biological functions of ORs within the gastrointestinal tract. Studies indicate that intestinal ORs exhibit distinct spatial distribution patterns across different gut segments and display cell-type specificity, particularly within enterocytes and enteroendocrine cells. These receptors function as versatile sensors capable of recognizing a wide variety of ligands, including exogenous dietary components, gut microbiota metabolites such as short-chain fatty acids, and endogenous small molecules like azelaic acid. Upon activation by specific ligands, intestinal ORs trigger intracellular signaling cascades, primarily involving the AC-cAMP-PKA pathway or calcium influx channels. A major focus of this review is to elucidate the molecular mechanisms by which these receptors regulate the secretion of gut hormones. Activation of specific ORs in enteroendocrine cells has been shown to stimulate the release of hormones such as glucagon-like peptide-1 (GLP-1), peptide YY (PYY), and serotonin (5-HT), thereby modulating systemic energy metabolism, glucose homeostasis, and gastrointestinal motility. Furthermore, the review addresses the critical roles of ORs in immune regulation and pathology. Evidence suggests that specific ORs contribute to the maintenance of intestinal immune homeostasis and may offer protection against inflammation. Beyond their involvement in inflammatory responses, ORs such as Olfr78 have been shown to regulate the differentiation and function of intestinal endocrine cells. Similarly, Olfr544 has been demonstrated to alleviate intestinal inflammation by remodeling the gut microbiome and metabolome. These findings collectively suggest that specific ORs hold promise as therapeutic targets for mitigating intestinal inflammation and maintaining gut homeostasis. Additionally, the review explores the emerging role of ORs in cancer. Although OR expression is often downregulated in tumor tissues compared to normal mucosa, activation of specific ORs by certain ligands can inhibit tumor cell proliferation and migration and induce apoptosis via pathways such as MEK/ERK and p38 MAPK. Conversely, other receptors, such as OR7C1, may serve as biomarkers for cancer-initiating cells. In conclusion, intestinal ORs represent a vital component of the gut’s sensory network. The review also discusses the translational potential of these findings. By elucidating the precise pairing relationships between dietary components and specific ORs, novel therapeutic strategies could be developed. Intestinal ORs may thus emerge as promising targets for nutritional and pharmacological interventions in metabolic diseases, inflammatory bowel diseases, and malignancies.
3.Jianpi Xiaoai Prescription Ameliorates Chemotherapy Resistance in Colon Cancer by Targeting FGF2 to Inhibit PI3K/Akt Signaling Pathway
Xiaolan JIAN ; Kangwen NING ; Jiaxiang YANG ; Shenglan KOU ; Wanting KUANG ; Ziqi WANG ; Yuqin TAN ; Puhua ZENG ; Lingjuan TAN ; Wei PENG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(6):120-130
ObjectiveTo explore the effect and mechanism of Jianpi Xiaoai prescription (JPXA) in ameliorating the 5-fluorouracil (5-FU) resistance of colon cancer. MethodsA HCT116/5-FU resistant cell line was established. Different concentrations (10%, 15%, 20%) of JPXA-containing serum and drug-free serum were used for intervention, and 10% fetal bovine serum (10% FBS), fibroblast growth factor receptor (FGFR) inhibitor (AZD4547), and recombinant fibroblast growth factor 2 (FGF2) were set as the control groups. Sensitive HCT116 cells were used in the FGF2 group, while HCT116/5-FU cells were used in other groups. Drug resistance, the level of FGF2 in the cell culture medium, the mRNA level of FGF2 in cells, and the protein levels of FGF2/FGFR and phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) were determined. The drug-resistant cells were transplanted into the axilla of nude mice to establish a tumor model. The modeled mice were allocated into model, JPXA (15 g·kg-1), 5-FU (0.02 g·kg-1), JPXA+5-FU (15 g·kg-1+0.02 g·kg-1), AZD4547 (0.012 5 g·kg-1), and AZD4547+5-FU (0.012 5 g·kg-1+0.02 g·kg-1) groups. The tumor growth and the protein levels of FGF/FGFR and PI3K/Akt in each group were observed. ResultsThe survival rate of HCT116/5-FU cells decreased in all the JPXA groups with different concentrations. The cell survival rate was decreased most obviously in the 20% JPXA group. The level of FGF2 in the cell culture medium and the mRNA level of FGF2 in cells of each JXPA group decreased, and the decrease was the most significant in the 20% group (P<0.01). HCT116/5-FU cells showed up-regulated protein levels of FGF2 and phosphorylated fibroblast growth factor receptor 1 (p-FGFR1), but down-regulated protein level of FGFR1 (P<0.01). JPXA down-regulated the expression of FGF2 and p-FGFR1 and up-regulated the expression of FGFR1 (P<0.05). In addition, JPXA down-regulated the expression levels of phosphorylated protein kinase B (p-Akt) and phosphorylated mammalian target of rapamycin (p-mTOR), while up-regulating the expression levels of Akt and Bcl-2-asociated death promoter (Bad) (P<0.05). Animal experiments showed that the JPXA combined with 5-FU significantly inhibited the growth of drug-resistant tumors, reduced the protein levels of FGF2, p-FGFR1, phosphorylated phosphatidylinositol-3-kinase (p-PI3K), p-Akt, and p-mTOR, and increased the expression of Bad. It indicated that JPXA can inhibit the FGF2/FGFR1 signaling in colon cancer and regulate PI3K/Akt and downstream signaling pathways. ConclusionJPXA can ameliorate the chemotherapy resistance of colon cancer through down-regulating FGF2 expression and inhibiting the activation of the PI3K/Akt signaling pathway.
4.Comparison of bioelectrical impedance analysis and dual energy X ray absorptiometry in measuring body composition among Tibetan children and adolescents
Chinese Journal of School Health 2026;47(4):569-573
Objective:
To compare the consistency between bioelectrical impedance analysis (BIA) and dual energy X ray absorptiometry (DXA) in measuring body composition among Tibetan children and adolescents and to explore the applicability of BIA in plateau region, so as to provide scientific and convenient body composition measurement support among children and adolescents.
Methods:
From May to June, 2022, a total of 344 Tibetan children and adolescents aged 6-17 years were selected from Golmud Municipal National Middle School and Changjiangyuan Nationality Primary School in Qinghai Province by cluster sampling method, and their fat mass, fat mass percentage and lean mass were measured by DXA and BIA. The consistency and correlation between the two methods were assessed by using the Wilcoxon rank-sum test, Spearman correlation analysis, intraclass correlation coefficient (ICC), and Bland-Altman analysis.
Results:
DXA measured fat mass and fat mass percentage were significantly higher than those obtained by BIA (6-12 years old: Z =9.91, 11.28; 13-17 years old: Z =9.02, 10.21), while lean mass and lean mass percentage were significantly lower than BIA results (6-12 years old: Z =-11.60, -11.30; 13-17 years old: Z =-10.77, -10.36) (all P < 0.05 ). The two methods showed strong correlations in fat mass and lean mass (all r >0.80, all ICC >0.90), but exhibited poor agreement in fat mass percentage and lean mass percentage (6-12 years old: Lin s CCC =0.64, 0.41; 13-17 years old: Lin s CCC = 0.79 , 0.35). Bland-Altman analysis showed that the difference between the two methods was negatively correlated with the average value in FM%(6-12 years old: r =-0.75, 13-17 years old: r =-0.79, both P <0.01).
Conclusion
BIA and DXA show high consistency in measuring body fat mass and lean body mass in Tibetan children and adolescents, although some bias is still present in certain individuals.
5.Mitochondial-located miRNAs in The Regulation of mtDNA Expression
Peng-Xiao WANG ; Le-Rong CHEN ; Zhen WANG ; Jian-Gang LONG ; Yun-Hua PENG
Progress in Biochemistry and Biophysics 2025;52(7):1649-1660
Mitochondria, functioning not only as the central hub of cellular energy metabolism but also as semi-autonomous organelles, orchestrate cellular fate decisions through their endogenous mitochondrial DNA (mtDNA), which encodes core components of the electron transport chain. Emerging research has identified microRNAs localized within mitochondria, termed mitochondria-located microRNAs (mitomiRs). Recent studies have revealed that mitomiRs are transcribed from nuclear DNA (nDNA), processed and matured in the cytoplasm, and subsequently transported into mitochondria. mitomiRs regulate mtDNA through diverse mechanisms, including modulation of mtDNA expression at the translational level and direct binding to mtDNA to influence transcription. Aberrant expression of mitomiRs leads to mitochondrial dysfunction and contributes to the pathogenesis of metabolic diseases. Restoring mitomiR expression to physiological levels using mitomiRs mimics or inhibitors has been shown to improve mitochondrial function and alleviate related diseases. Consequently, the regulatory mechanisms of mitomiRs have become a major focus in mitochondrial research. Given that mitomiRs are located in mitochondria, targeted delivery strategies designed for mtDNA can be adapted for the delivery of mitomiRs mimics or inhibitors. However, numerous intracellular and extracellular barriers remain, highlighting the need for more precise and efficient delivery systems in the future. The regulation of mtDNA expression mediated by mitomiRs not only expands our understanding of miRNA functions in post-transcriptional gene regulation but also provides promising molecular targets for the treatment of mitochondrial-related diseases. This review systematically summarizes recent research progress on mitomiRs in regulating mtDNA expression and discusses the underlying mechanisms of mitomiRs-mtDNA interactions. Additionally, it provides new perspectives on precision therapeutic strategies, with a particular emphasis on mitomiRs-based regulation of mitochondrial function in mitochondrial-related diseases.
6.Analyzing the evaluation results of healthy enterprises in Hubei Province from 2020 to 2023
Zhe PENG ; Jian HUANG ; Sheng LIU ; Zhongfa JIANG ; Yongxiang YAO ; Liangying MEI
China Occupational Medicine 2025;52(3):299-303
Objective To analyze the evaluation and influencing factors of healthy enterprises in Hubei Province from 2020 to 2023. Methods A total of 351 enterprises participated in the healthy enterprise evaluation in Hubei province were selected as the study subjects using the judgmental sampling method. The differences in evaluation results including scales, industry sector, and ownership type of the enterprises were compared. Results The median and the 25th and 75th percentiles [M (P25, P75)] of the evaluation score among the 351 enterprises was 869 (838, 941) points. The evaluation pass rate was 82.3%. The M(P25, P75) of scores for the management system, health environment, health management and services, health culture, and health outcome review were 183 (174, 192), 190 (181, 198), 340 (321, 376), 133 (122, 142), and 26 (24, 28) points, with the score percentage of 91.5%, 86.4%, 85.0%, 88.7%, and 86.7%, respectively. The deduction rate exceeded 50.0% in six items, which predominantly concentrated within the primary indicator of the health management and services, among the tertiary indicators. The result of multiple linear regression analysis revealed that smaller enterprises had significantly lower evaluation scores (P<0.05), and domestically funded enterprises scored significantly lower than those with investment from Hong Kong, Macao and Taiwan, or foreign investments (all P<0.05). Conclusion Health management and services represent a weak area in healthy enterprise development in Hubei Province. It was suggested to improve policy incentives and support for medium-, small- and micro-sized enterprises, and domestically funded enterprises, to enhance healthy enterprise development levels.
7.Oxidative Stress-related Signaling Pathways and Antioxidant Therapy in Alzheimer’s Disease
Li TANG ; Yun-Long SHEN ; De-Jian PENG ; Tian-Lu RAN ; Zi-Heng PAN ; Xin-Yi ZENG ; Hui LIU
Progress in Biochemistry and Biophysics 2025;52(10):2486-2498
Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, functional impairment, and neuropsychiatric symptoms. It represents the most prevalent form of dementia among the elderly population. Accumulating evidence indicates that oxidative stress plays a pivotal role in the pathogenesis of AD. Notably, elevated levels of oxidative stress have been observed in the brains of AD patients, where excessive reactive oxygen species (ROS) can cause extensive damage to lipids, proteins, and DNA, ultimately compromising neuronal structure and function. Amyloid β‑protein (Aβ) has been shown to induce mitochondrial dysfunction and calcium overload, thereby promoting the generation of ROS. This, in turn, exacerbates Aβ aggregation and enhances tau phosphorylation, leading to the formation of two pathological features of AD: extracellular Aβ plaque deposition and intracellular neurofibrillary tangles (NFTs). These events ultimately culminate in neuronal death, forming a vicious cycle. The interplay between oxidative stress and these pathological processes constitutes a core link in the pathogenesis of AD. The signaling pathways mediating oxidative stress in AD include Nrf2, RCAN1, PP2A, CREB, Notch1, NF‑κB, ApoE, and ferroptosis. Nrf2 signaling pathway serves as a key regulator of cellular redox homeostasis, exerts important antioxidant capacity and protective effects in AD. RCAN1 signaling pathway, as a calcineurin inhibitor, and modulates AD progression through multiple mechanisms. PP2A signaling pathway is involved in regulating tau phosphorylation and neuroinflammation processes. CREB signaling pathway contributes to neuroplasticity and memory formation; activation of CREB improves cognitive function and reduce oxidative stress. Notch1 signaling pathway regulates neuronal development and memory, participates in modulation of Aβ production, and interacts with Nrf2 toco-regulate antioxidant activity. NF‑κB signaling pathway governs immune and inflammatory responses; sustained activation of this pathway forms “inflammatory memory”, thereby exacerbating AD pathology. ApoE signaling pathway is associated with lipid metabolism; among its isoforms, ApoE-ε4 significantly increases the risk of AD, leading to elevated oxidative stress, abnormal lipid metabolism, and neuroinflammation. The ferroptosis signaling pathway is driven by iron-dependent lipid peroxidation, and the subsequent release of lipid peroxidation products and ROS exacerbate oxidative stress and neuronal damage. These interconnected pathways form a complex regulatory network that regulates the progression of AD through oxidative stress and related pathological cascades. In terms of therapeutic strategies targeting oxidative stress, among the drugs currently used in clinical practice for AD treatment, memantine and donepezil demonstrate significant therapeutic efficacy and can improve the level of oxidative stress in AD patients. Some compounds with antioxidant effects (such asα-lipoic acid and melatonin) have shown certain potential in AD treatment research and can be used as dietary supplements to ameliorate AD symptoms. In addition, non-drug interventions such as calorie restriction and exercise have been proven to exerted neuroprotective effects and have a positive effect on the treatment of AD. By comprehensively utilizing the therapeutic characteristics of different signaling pathways, it is expected that more comprehensive multi-target combination therapy regimens and combined nanomolecular delivery systems will be developed in the future to bypass the blood-brain barrier, providing more effective therapeutic strategies for AD.
8.Analysis of food poisoning event by type F Clostridium perfringens in a school
Chinese Journal of School Health 2025;46(10):1493-1497
Objective:
To understand the epidemiological and etiological characteristics of food poisoning event occurred in a school in Hangzhou, Zhejiang, so as to provide reference for the scientific management of related emergencies.
Methods:
By determining the nature of the event through epidemiological investigation, a case control study was carried out to spot suspicious food in May 2024. The hygienic investigation was conducted to find out possible pollution links and factors, patients and canteen practitioners anal swab, canteen retention samples, catering link daub and other specimens were collected ,for rapid pathogen screening. And the suspected pathogen Clostridium perfringens (CP) were isolated and identified according to the screening results, and toxin gene detection and whole genome sequencing and cluster analysis of CP isolated strains were carried out.
Results:
The incident resulted in 45 people experiencing gastrointestinal symptoms, such as diarrhea and abdominal pain. The suspicious food was tomato scrambled eggs and corn ribs provided by the student canteen for lunch on May 29. A hygiene investigation found that there was a risk of contamination in the food processing, preparation and storage. A total of 46 anal swabs and 10 canteen retention samples were positive for CP 16 S, 59 strains of CP were isolated from 27 samples, 10 cases and 1 practitioner isolate were positive for CPE ( cpe ) (F mode), and their whole genome evolution analysis was conducted based on the same source.
Conclusions
The food poisoning event is caused by CP infection carrying CPE ( cpe ) (F mode), and the possible sources of outbreak are the carriers of the CP by employees. It is recommended that cafeteria staff strengthen training on common foodborne diseases and conduct regular monitoring of pathogens.
9.Tongnao Huoluo Liyan acupuncture combined with rehabilitation training for post-stroke dysphagia: a randomized controlled trial.
Jiemiao XU ; Jian LIU ; Yongjun PENG
Chinese Acupuncture & Moxibustion 2025;45(4):435-441
OBJECTIVE:
To observe the efficacy of the Tongnao Huoluo Liyan (unblocking brain, activating collaterals and relaxing throat) acupuncture combined with rehabilitation training for post-stroke dysphagia (PSD).
METHODS:
A total of 92 PSD patients were randomly assigned to an observation group (46 cases, 1 case was discontinued) and a control group (46 cases, 1 case was discontinued, 1 case dropped out). The patients in the control group received rehabilitation training, including low-frequency neuromuscular electrical stimulation for swallowing, lip and tongue movement training, and oral sensory function training, once daily, five times per week, for four weeks. The patients in the observation group received the Tongnao Huoluo Liyan acupuncture method in addition to the same rehabilitation training. Acupoints included Lianquan (CV23), bilateral Jia Lianquan, Jinjin (EX-HN12), Yuye (EX-HN13), Baihui (GV20), Shuigou (GV26), and bilateral Neiguan (PC6), once daily, five times per week, for four weeks. Before and after treatment, Kubota water stvallowing test grading, standardized swallowing assessment (SSA) scores, Fujishima Ichiro swallowing efficacy scores, and swallowing quality of life questionnaire (SWAL-QOL) scores were assessed in both groups. Surface electromyography (sEMG) was used to evaluate the average amplitude (AEMG) and mean swallowing time of the suprahyoid and infrahyoid muscle groups.
RESULTS:
After treatment, the proportion of patients classified as Grade Ⅰ or Ⅱ in the Kubota water stvallowing test was increased in both groups (P<0.05), with better results in the observation group compared to the control group (P<0.05). Compare before treatment, SSA scores were decreased in both groups after treatment (P<0.05), with lower scores in the observation group than in the control group (P<0.05). Compare before treatment, Fujishima Ichiro swallowing efficacy scores and SWAL-QOL scores were improved in both groups after treatment (P<0.05), with significantly higher scores in the observation group than those in the control group (P<0.05). Compare before treatment, AEMG values of the Submental musckes and infrahyoid muscles groups were increased (P<0.05), and mean swallowing time was decreased (P<0.05) in both groups after treatment. The observation group showed greater increases in AEMG values and shorter mean swallowing times compared to the control group (P<0.05). The total effective rate was 97.8% (44/45) in the observation group, higher than 84.1% (37/44) in the control group (P<0.05).
CONCLUSION
The Tongnao Huoluo Liyan acupuncture combined with rehabilitation training could enhance the contraction function in swallowing-related muscle groups, facilitate hyoid and laryngeal elevation, restore swallowing function, and improve patients' quality of life. This combined treatment approach is superior to rehabilitation training alone.
Humans
;
Female
;
Acupuncture Therapy
;
Male
;
Middle Aged
;
Deglutition Disorders/physiopathology*
;
Aged
;
Stroke/complications*
;
Acupuncture Points
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Adult
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Treatment Outcome
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Stroke Rehabilitation
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Combined Modality Therapy
10.Research progress of the dopamine system in neurological diseases.
Yu-Qi NIU ; Jin-Jin WANG ; Wen-Fei CUI ; Peng QIN ; Jian-Feng GAO
Acta Physiologica Sinica 2025;77(2):309-317
The etiology of nervous system diseases is complicated, posing significant harm to patients and often resulting in poor prognoses. In recent years, the role of dopaminergic system in nervous system diseases has attracted much attention, and its complex regulatory mechanism and therapeutic potential have been gradually revealed. This paper reviews the role of dopaminergic neurons, the neurotransmitter dopamine, dopamine receptors and dopamine transporters in neurological diseases (including Alzheimer's disease, Parkinson's disease and schizophrenia), with a view to further elucidating the disease mechanism and providing new insights and strategies for the treatment of neurological diseases.
Humans
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Dopamine/metabolism*
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Nervous System Diseases/physiopathology*
;
Parkinson Disease/physiopathology*
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Receptors, Dopamine/metabolism*
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Dopaminergic Neurons/physiology*
;
Dopamine Plasma Membrane Transport Proteins/metabolism*
;
Alzheimer Disease/physiopathology*
;
Schizophrenia/physiopathology*
;
Animals


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