Subjects: Biology >> Biochemistry submitted time 2024-04-24
Abstract： How to differentiate the diagnosis of depression and bipolar disorder has always been an important problem that needs to be solved urgently in clinical practice. In this study, from the perspective of urine proteomics, urine samples of similar age were collected from two hospitals to investigate the candidate biomarkers for differentiating the diagnosis of depression and bipolar disorder using both group analysis and one-to-many analysis. The experimental results of the paired group analysis showed that 108 differential proteins were identified in the depressed group compared to the bipolar group under strict screening conditions with screening criteria of FC ≥ 2 or ≤ 0.5 and a two-tailed unpaired t-test of P < 0.01, with an average of 3.7 randomly generated differential proteins, and a confidence level of 96.6 % for the correlation between these proteins and the disease difference. In the one-to-many analysis, 24 differential proteins were co-identified by the samples of 13 depressed patients, 16 of which showed a completely consistent trend of expression changes in all depressed patients studied, and 6 of which were associated with immunoglobulins; 41 differential proteins were co-identified by the samples of 12 depressed patients out of 13, and 19 of which showed a completely consistent trend of expression change in the These results reflect the strong consistency of differential proteins between the two groups of patients. 12 or more samples from depressed patients were enriched for differential proteins related to multiple biological processes and signaling pathways associated with the immune system, which is consistent with previous studies: immune mechanisms may be one of the pathogenetic mechanisms of major depression and that drugs with major immune targets can improve depressive symptoms. In the future, it may be possible to observe the immune status of patients with depression to provide direction and basis for the precise treatment of depression. The results of this paper show that urine proteomics can differentiate between depression and bipolar disorder, suggest possible mechanisms and potential targets for the treatment of depression and bipolar disorder, and provide a tool for future differential diagnosis and precision treatment of the diseases.
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Awaiting Review
Subjects: Biology >> Biochemistry Subjects: Biology >> Molecular Biology submitted time 2024-01-25
Abstract： Objective: To explore the possible effects of different sweet taste substances on the body by analyzing the changes of urinary proteome in mice after self-consumption of different sweet taste substances.
Methods: Urine samples of C57BL/6l mice were collected before and after self-consumption of sweet substances, including sucrose, stevia glycosides, acesulfame and sucralose, which are widely used in the world and can cause the preference reaction of mice. Among them, the concentration of non-nutritive sweeteners was selected as the concentration that has been shown to have the strongest preference reaction of mice. Label-free quantitative proteomics using high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for analysis. Differential proteins of urine proteome were screened in groups for analysis of protein functions and biological pathways. The urine proteome of single mice before and after self-consumption of sweet substances was compared, and the common differential proteins were counted; and the different sweet substances were compared horizontally.
Results and conclusions: Urine proteome can reflect the body changes of mice after self-consumption of sweet substances. And the effects of different sweet substances on urine proteome were different. Among the four sweet substances, sucralose caused the most similar changes in the body compared with sucrose. Compared with sucrose, stevia glycosides caused the most different changes in the body. The body changes caused by sucrose, acesulfame and sucralose are similar, but the body changes caused by stevia glycoside are different from other sweet substances. After self-consumption of the four sweet substances, the urine proteome differential proteins in mice all had proteins that had been reported to be related to brain reward circuitry, while only the urine proteome differential proteins after self-consumption of sucrose, acesulfame and sucralose were mainly related to metabolic processes. Urine proteomic differential proteins after acesulfame of stevia glycoside were mainly related to nucleosome assembly and gene expression.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2024-01-20
Abstract： Do rats have corresponding changes in their urinary proteome when smelling odors? Do sniffing different odors produce different changes? In this study, urine samples were collected from six rats after smelling sesame oil and essential balm for three days, and on the third and fourth days, and the samples were analyzed in groups and single before and after comparisons using LC-MS/MS technology. The identified differential proteins were also compared with those produced by the growth and development of rats of the same age group to exclude the influence of growth and development on the results of this experiment. The experimental results showed that comparing the urine protein groups of Day0 and Day4 of the sesame oil group, 143 differential proteins could be identified after screening, and the average number of randomly generated differential proteins was 7.32, at least 94.88% of the differential proteins were not randomly generated. Upon comparative analysis in groups and singly before and after, the same odor showed more consistent changes, and differential proteins such as low-density lipoprotein receptor-related protein 2 and fetuin B, a biomarker of COPD, which are associated with olfactory production, were identified in the sesame oil group, while uteroglobulin, trichothecene factor 3, and visfatin 2 were identified in the essential balm group, which had significant changes and were related to the production of olfactory sensation. It is noteworthy that we identified odor-binding protein 2A again in the essential balm group, simultaneously present in the differential proteins produced by a single before-and-after comparison in four rats, which is consistent with the results presented in the e-cigarette model. This study demonstrates that odor affects the urinary proteome of rats, with different odors affecting it differently. This provides a new approach to explore the biological process of olfaction.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2024-01-19
Abstract： Zinc is an essential element for maintaining normal physiological function in living organisms. In this study, 82 mg/kg·d zinc gluconate (equivalent to 11.7 mg/kg·d zinc) was intragastrically administered to rats for 4 days, and the urine proteome of rats before and after short-term intragastric administration of zinc gluconate was compared and analyzed. Many differential proteins have been reported to be zinc related, such as mucin-2 (MUC-2) (14 times before compared with after gavage, p = 0.005) and transthyretin (3.9 times after gavage compared with before gavage, p = 0.0004). Biological processes enriched in differential proteins (e.g., regulation of apoptosis process, immune system process, etc.), molecular functions (e.g., calcium binding, copper binding, signaling receptor activity, etc.), KEGG pathways (e.g., complement and coagulation cascades, PI3K-Akt signaling pathway, etc.) showed correlation with zinc. In this study, we explore the overall effect of zinc on the body from the perspective of urine proteomics, which is helpful to deeply understand the biological function of zinc and broaden the application potential of urine proteomics.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2024-01-18
Abstract： Calcium is an essential element for maintaining the normal physiological function of organisms. In this study, 3225 mg/kg · d calcium gluconate (equivalent to 300 mg/kg · d calcium) was intragastrically administered to rats for 4 days, and the urine proteome of rats was analyzed. Many differential proteins have been reported to be calcium related, such as Regucalcin (2.6 times higher after gavage than before gavage, p = 0.022), transmembrane protein 132A (8.2 times higher after gavage than before gavage, p = 0.009), creatine kinase (17.5 times higher before gavage than after gavage, p = 0.006), and claudin-3 (13.3 times higher before gavage than after gavage, p = 0.037). Differential protein enriched KEGG pathways included calcium signaling pathways, and biological processes and molecular functions also showed correlation with calcium. In this study, from the perspective of urine proteomics to explore the overall impact of calcium on the body, it is helpful to deeply understand the biological function of calcium and broaden the application potential of urine proteomics.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2024-01-04
Abstract： Iron is an essential trace element to maintain the normal physiological function of organisms. No studies have investigated the overall effect of iron on the body from the perspective of urine proteome. In this study, the urine proteome of rats before and after short-term intragastric administration of polysaccharide-iron complex (28mg/kg·d iron, which is equivalent to the dose of anemia prevention in adults) was compared and analyzed by using two analysis methods: individual comparison and group comparison. Many different proteins were reported to be related to iron, including 2', 3' -cyclic nucleotide 3' -phosphodiesterase (CNPase) (7.7 times higher than that after gavage, p=0.0039), p38 (14.5 times higher than that before gavage, p=0.003), etc. In the individual comparison, Hepcidin was up-regulated in 4 rats simultaneously. The biological processes of differential protein enrichment include carbohydrate metabolism, iron ion reaction, apoptosis regulation, hematopoietic progenitor cell differentiation, etc. Molecular functions (e.g., complement binding, hemoglobin binding, etc.), KEGG pathways (e.g., complement and coagulation cascade, cholesterol metabolism, malaria, etc.) have also been shown to be associated with iron. This study contributes to the in-depth understanding of the biological function of iron from the perspective of urine proteomics, and provides a new research perspective for the prevention, diagnosis, treatment and monitoring of iron-related disorders.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry Subjects: Biology >> Molecular Biology submitted time 2024-01-02
Abstract： Objective: Comparison of urine proteome between obese people and normal people.
Methods: Urine samples from obese and normal people were collected and identified by non-label quantitative proteomics using high performance liquid chromatography tandem mass spectrometry (LC-MS/MS). The difference proteins of urine proteome between obese and normal people were screened for protein function and biological pathway analysis. The urine proteome of obese individuals was compared with that of normal people, and the common differential proteins were counted to analyze the protein function and biological pathways. Reported biomarkers of obesity were searched in the urine proteome of obese individuals.
Results: 38 different proteins can be identified in the urine proteome of obese people compared with normal people, some of which have been reported to be related to metabolism and obesity, and the biological processes of differential proteins are also related to metabolism and other processes. 8 common differential proteins in the urine proteome of obese individuals and normal people, among which some proteins have been reported to be related to metabolism and obesity, and the biological processes of differential proteins are also related to metabolism and other processes. Among the differential proteins in the urine proteome of obese individuals compared with the normal people, the reported obesity biomarkers can be matched.
Conclusions: The urine proteome can distinguish the obese people, and the differential proteins in the urine proteome have key proteins that are known to be related to obesity and metabolism, and the biological processes of differential proteins also related biological processes such as nutrition and metabolism. Urine proteome has the potential to explore the pathogenesis of obesity and provide personalized treatment.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry Subjects: Biology >> Molecular Biology submitted time 2023-11-16
Abstract： Objective: To compare urine proteome changes in the first two days after mating behavior in male rats.
Methods: The urine samples of Sprague-Dawley rats on the day of mating and the day after mating were collected and analyzed by non-label quantitative proteomics by high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the differential proteins (FC > 1.5 or < 0.67) in the urine proteome were screened. P<0.050) protein function and biological pathways were analyzed.
Results: 43 different proteins were identified in the urine proteome between the day after mating and the day after mating. By searching the Uniprot database and Pubmed database and related literature reports, nearly two-thirds of the differential proteins were associated with spermatogenesis.
Conclusions: The urine proteome changed the day after mating compared to the day after mating, and some of the known functions of the changed proteins were associated with spermatogenesis.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany Subjects: Biology >> Biochemistry submitted time 2023-10-23
Abstract： The protein-protein interactions (PPIs) have a pivotal role in plant cells. There are numerous methods, in vivo or in vitro, have been developed to investigate the PPIs. The yeast mating-based Split-Ubiquitin System (mbSUS) is an alternative method of classic yeast-two-hybrid (Y2H) method. The mbSUS assay is not only as fast and inexpensive as the Y2H method, but also suitable for membrane proteins investigation with lower false positive rate. The recently improved mbSUS assay is suitable for the determination of PPIs among membrane proteins and soluble proteins, and successful used for detecting the interaction between ion channels and vesicle traffic proteins. Here, we describe the principles, protocols and experiment notes for mbSUS assay, providing an alternative method for PPI research in plants.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2023-10-11
Abstract： Methods: The urine samples of Recurrent spontaneous abortion (RSA) model mice during implantation (E3.5 and E4.5) and normal pregnant mice during implantation (E3.5 and E4.5) were collected. The protein function and biological pathways were analyzed by non-label quantitative proteomics using high performance liquid chromatography tandem mass spectrometry (LC-MS/MS). Differential proteins (FC > 1.5 or < 0.67, P<0.050) in the urine proteome were screened.
Results: There were 4 mice in RSA model, none of which gave birth. There were 3 normal pregnant mice, and 7, 8 and 9 litters were born respectively at E21. At E3.5, 23 differential proteins could be identified, and at E4.5, 21 differential proteins could be identified. According to Uniprot database and Pubmed database search and related literature reports, nearly half of the differential proteins were associated with implantation. The differential proteins were enriched into a large number of biological pathways related to the implantation process through the David database.
Conclusions: In other words, when the level of human villus gonadotropin in the blood of pregnant women has not changed, and it is impossible to observe and accurately judge pregnancy by existing means, compared with normal pregnant mice, the urine proteome of RSA model mice has changed during the implantation stage, and the known functions of some of the changed proteins are related to implantation.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2023-02-24
Abstract： This study aimed to explore the effect of massage on the urine proteome of healthy people. In this study, participants underwent 1-hour whole body massage. Urine samples were collected at 0, 2, and 24h after the massage and urine proteins were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Compared with the control (before massage), 41 differential proteins were identified in the group 2h after the massage, the random mean number of differentially produced proteins was 11 with 73% confidence, and the biological process of protein enrichment was catecholamine biosynthesis, which was related to the promotion of metabolism and the regulation of neural activities. While 29 differential proteins were identified in the group 24h after the massage, the random average number of differential proteins produced was 10, with the confidence of the difference decreased to 65%, and the effective biological process could not be enriched at this time. The results suggested that the difference in urine protein was greater at 2h after the massage and gradually decreased at 24h after the massage. The proteome of urine may reflect changes in the body following minor massage stimuli, providing a potential way to evaluate the effects of massage therapy.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2023-01-13
Abstract： In this study, we constructed a rat e-cigarette model and collected urine samples before, during, and after e-cigarette smoking in rats, that is, on days 0, 3, 12, 15, and 17, to explore e-cigarettes from the perspective of urine proteomics. In order to exclude the influence of individual differences, the experiment used a single rat before and after control for analysis, while the control group was set up to rule out differences caused by rat growth and development. The results showed that after smoking e-cigarettes under the same conditions, the differential proteins produced by rats had strong individual differences. We found that six experimental rats combined before and after controls identified fetuin-B, a biomarker of COPD, and annexin A2, which is recognized as a multiple tumor marker, among the differential proteins produced by rats on day 3 of e-cigarette smoking. Odorant binding proteins expressed in the olfactory epithelium were also found to be present in the urine proteome and were significantly upregulated in this study. We also found evidence that smoking e-cigarettes affects the immune system, cardiovascular system, respiratory system, etc. in both the resulting differential proteins and enriched signaling pathways, providing clues for further exploration of the mechanism of e-cigarettes on the human body.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-09-20
Abstract： The fear of startle is generated in the brain, and urine proteomics was used to explore whether this fear can be detected in the urine. The combination of natural enemy odor and sound stimulation were used to establish a rat model of startle. Urine samples were collected before and after startle and proteomic analysis was performed. The results showed that 22 differential proteins were identified after startle, and the biological pathways enriched in these differential proteins were related to neurotransmitter transport and glucose transmembrane transport, which may be the manifestations of nervous tension caused by startle. Before-after study in single rat was performed and found that there was one differential protein identified samely in five rats, in addition, 19 differential proteins were identified samely in four of five rats, and these proteins were associated with the change of nerve, motion, metabolism and blood pressure, which include catalytic subunits and regulatory subunits of glutamate-cysteine ligase, which realted to the function of startle. These results laid the foundation for the research of startle mechanism, and to find medicine for the treatment of psychological terror target provides a new method. At the same time, it fully illustrates the sensitivity of urine and opens up a new field for the exploration of urine.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-05-16
Abstract：本文是哈尔滨工业大学（威海）生物化学设计性实验论文，实验采用 2 , 6-二氯靛酚法测定了 维生素饮料和泡腾片中维生素 C 含量，讨论了预制维生素饮料与泡腾片泡腾溶液作为维生素C 补剂的可行性，旨在为相关生物化学课程设计性实验提供参考。 结果表明每毫升脉动饮料含有0.566mg 还原型维生素C，每克泡腾片含84.86mg 还原型维生素C。从补充维生素 C 的角度看 , 每日饮用一个1L 装脉动饮料或冲泡饮用一个泡腾片尚未超过维生素C 食用最高限制，是膳食之外补充维生素C 的优良选择。
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-04-24
Abstract：
[Objective] To explore the effect of traditional Chinese medicine on the urine proteome of healthy rats.
[Methods] In this study, Intragastric administration rat models were established by two traditional Chinese medicines (Compound Danshen Dropping Pills and Huoxiangzhengqi Oral Liquid). Urine samples were collected from rats before and after intragastric administration. Liquid chromatography-mass spectrometry (LC-MS/MS) was used to screen the urine differential proteins of rats before and after intragastric administration and analyze the biological pathway of differential proteins.
[Results] Urine proteome can reflect the changes before and after 14 days of intragastric administration of Compound Danshen Dropping Pills, and the biological pathways enriched by differential proteins are related to their mechanism of action in the treatment of cardiovascular diseases, such as glycolysis, lipid metabolism.
[Conclusions] Urine proteomics can directly and systematically reflect the overall impact of traditional Chinese medicine on the body, and provides a new method to study the efficacy of traditional Chinese medicine.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry Subjects: Information Science and Systems Science >> Systematology submitted time 2022-04-05
Abstract：
For the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine-2,4-dioxygenase (HOD), the dioxygen (O2) dependent steps are rate-limiting along with a spin state crossover to the singlet spin state. Here, the primary triplet O2 molecule activation on the 2-methyl-3-hydroxy-4(1H)-quinolone (MHQ) is investigated, and the catalytic role of the intersystem crossing effects is highlighted by directly comparing results from the Born-Oppenheimer dynamics and non-adiabatic surface hopping dynamics. This work confirms non-adiabatic dynamical effects are essential to modulate the O2 activation on the substrate MHQ. The time scale of the equilibration and conversion from triplet to singlet state should be in the range of a few hundreds of femtoseconds. We hope this work provides us a fresh look at the underlying physics of dioxygen activation reactions involving more than one spin state.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-04-04
Abstract：
[Objective] The changes in the immune system in urine proteome were observed by injecting bovine serum albumin and aluminum hydroxide adjuvant into rats.
[Methods] In this study, bovine serum albumin and aluminum hydroxide adjuvant were injected into rat thigh muscle, urine was collected, differential proteins were identified by liquid chromatography-mass spectrometry (LC-MS / MS), and biological pathways of differential proteins were analyzed by IPA software to observe the changes of the immune system in rat urinary protein.
[Results] Fifteen rats were intramuscularly injected with normal saline, aluminum hydroxide adjuvant, bovine serum albumin, aluminum hydroxide adjuvant, and bovine serum albumin (BSA) mixture to construct the models of the control group, adjuvant group, BSA group, and mixed group. Comparing the different proteins between different groups to get the relevant biological pathways, it was found that adjuvants can be observed in urine to help bovine serum albumin stimulate the immune system to respond earlier. It was also observed in urine that the mixed group successively stimulated immune-related pathways such as inflammatory response, T cell activation, antigen-presenting cell-related pathways, and B cell-related pathways.
[Discussion] We can observe the changes in the immune system from urine proteome in the early stage, which provides some new clues and a basis for future research on the immune system and even accelerates the research and development of a vaccine.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-04-01
Abstract：目的：怀孕是身体生理状态产生极大变化的过程，正常的妊娠过程对保证胎儿发育正常和健康的母体非常重要，我们试图探索尿蛋白组变化能否反映妊娠过程。 方法：我们分别收集孕鼠妊娠0天、2天、12天、14天、16天、18天和20天的尿样，通过LC-MS高通量质谱分析不同时间的尿蛋白组，分别与妊娠第0天比较得到的差异蛋白进行生物学通路分析。 结果：妊娠第2天尿蛋白组的变化与胚胎着床、胎盘的分化相关的通路，妊娠后期（E16和E18），尿富集到与器官发育相关的通路，主要是肺发育相关的通路。有趣的是，据之前的报道，尿里发现着床相关的通路的时间点刚好在大鼠着床期内；大鼠肺发育主要是在妊娠后期(E11-E21)，我们发现尿里肺发育相关的通路也与这一时期相符。此外，从妊娠后期到分娩，发现凝血系统相关的过程不断显著，与之前报道过的妊娠过程中凝血功能不断增强的趋势一致。 结论: （1）尿蛋白组可以反映正常妊娠过程；（2）尿可能成为监测妊娠过程的有效策略。
Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-03-14
Abstract：
Objective This study focuses on the most important concern of surgeons - whether they resected all the tumors. Urine may reflect early changes associated with physiological or pathophysiological processes. Based on the above ideas, we have conducted some experiments to explore changes in the urine proteome urine proteomes between tumor-bearing mice to tumor-resected mice. Method The tumor-bearing mouse model was established with MC38 mouse colon cancer cell, and the mice were divided into the healthy control group, tumor complete resection group, and the tumor non-resection group. Urine was collected on the 7 days and 30 days after resection. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify the urine proteome and then analyze differential proteins and biological pathways. Results (1) 7 days after the tumor removal surgery between the complete resection group and the non-resection group, there are 20 differential proteins that can distinguish the two groups. The biological process includes circadian rhythm, Notch signaling pathway, leukocyte cell-cell adhesion, heterophilic cell#2;cell adhesion via plasma membrane cell adhesion molecules. (2) 30 days after the tumor removal surgery between the complete resection group and the non-resection group, there are 33 differential proteins that can distinguish the two groups. The biological process includes cell adhesion, complement activation, the alternative pathway, immune system process, angiogenesis. (3) There was no significant difference between the two groups at 30 days after the tumor removal surgery between the complete resection group and the healthy control group. Conclusion The changes of urine proteome can reflect tumor with surgical removal or not.
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Peer Review Status:Awaiting Review
Subjects: Biology >> Biochemistry submitted time 2022-03-11
Abstract：
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Peer Review Status:Awaiting Review
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