scholarly journals Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

2021 ◽  
Author(s):  
Shengbo Wang ◽  
David García-Seisdedos ◽  
Ananth Prakash ◽  
Deepti Jaiswal Kundu ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Protein Expression ◽  
Rat Tissues ◽  
Protein Abundance ◽  
Proteomics Data ◽  
Pathway Enrichment ◽  
Expression Atlas ◽  
Organ Specific ◽  
High Level ◽  
Widespread Dissemination

The increasingly large amount of public proteomics data enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contains 23 individual datasets, which have a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We compared protein expression between the different organs, including the distribution of proteins across them. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples. Finally, it should be noted that protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

scholarly journals An integrated view of baseline protein expression in human tissues

2021 ◽  
Author(s):  
Ananth Prakash ◽  
David García-Seisdedos ◽  
Shengbo Wang ◽  
Deepti Jaiswal Kundu ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Protein Expression ◽  
Large Scale ◽  
Expression Data ◽  
Healthy Human ◽  
The Public ◽  
Pathway Enrichment ◽  
Expression Atlas ◽  
Consistent Manner ◽  
Organ Specific ◽  
Structural Region

AbstractThe availability of proteomics datasets in the public domain, and in the PRIDE database in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein expression data in a consistent manner. We have reanalysed 25 public proteomics datasets from healthy human individuals, to assess baseline protein abundance in 32 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 68 healthy tissues, corresponding to 3,167 mass spectrometry runs covering 501 samples, coming from 492 individuals.We compared protein expression between the different organs, studied the distribution of proteins across organs, and identified proteins, as well as their isoforms, that are uniquely expressed in certain organs. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein expression results into the resource Expression Atlas, where it can be accessed and visualised either individually or together with gene expression data coming from transcriptomics datasets.

COGNITIVIZATION — THE NEXT STAGE OF INFORMATIZATION OF EDUCATION

2018 ◽  
pp. 5-11
Author(s):  
A. S. Christochevskaya ◽  
S. A. Christochevsky
Keyword(s):  
Comparative Analysis ◽  
Learning Resources ◽  
Technical Base ◽  
Initial Stage ◽  
New Knowledge ◽  
Good Material ◽  
E Learning ◽  
New Material ◽  
High Level ◽  
Paper Method

Informatization of education has been going on for 30 years. During this time, a good material and technical base appeared in schools, there are repositories of e-learning resources to which teachers have access. However, it is difficult to use these e-learning resources due to their too large number and not always high level. It is advisable to introduce a system of reviews and recommendations, to conduct a comparative analysis, as well as to make reviews of resources on a particular subject/topic. In addition, the demand for e-learning resources is affected by the fact that education authorities encourage not so much the use of e-learning resources as their development by the teacher himself. In general, the load on teachers has increased instead of the promised saving of time and effort when using the e-learning resources. At the same time, many e-learning resources are not very effective, since they do not meet the requirements of cognitiveness (they contribute not to learning, but to simple memorization of the material). It is necessary to explore the process of learning new material: this will allow you to create cognitive e-learning resources and other resources that would help you with equal probability to successfully acquire new knowledge for students belonging to different psycho-types. At the initial stage of the study of any subject, it is more expedient to use the usual “paper” method, that is, a textbook and not overload the student’s brain with excessive information. Only when he has mastered the basic provisions, we can turn to e-learning resources, bearing in mind that they must be cognitive, that is, they are aimed at logical perception and rapid intuitive learning, only in this case e-learning resources can be considered effective. The conclusion is formulated that cognitiveness is the next stage of informatization of education after the stage of electronization.

OPERATIONS FOR ANEURISM OF THE ABDOMINAL AORTIC DEPARTMENT - RESECTION WITH THE FOLLOWING PROSTHETICS AND ENDOPROSTHETICS: A COMPARATIVE ANALYSIS OF COMPLICATIONS

2020 ◽  
pp. 43-49
Author(s):  
Андрей Анатольевич Иванов ◽  
Александр Иванович Жданов ◽  
Максим Сергеевич Шевелин ◽  
Александр Сергеевич Брежнев
Keyword(s):  
Comparative Analysis ◽  
Postoperative Complications ◽  
Statistical Significance ◽  
Aortic Aneurysms ◽  
Surgical Interventions ◽  
Vein Thrombosis ◽  
Scientific Hypothesis ◽  
Abdominal Aortic ◽  
Life Threatening ◽  
High Level

В статье представлены данные оригинального исследования по улучшению хирургического лечения аневризм брюшного отдела аорты. С этой целью произведен сравнительный анализ двух альтернативных друг другу операций: 1) резекции аневризмы с последующим протезированием аорты; 2) эндопротезирования аорты. Сформулировано научное предположение о том, что замена «классических» операций резекции аневризмы на «альтернативные» операции эндопротезирования приведет к принципиальному снижению уровня послеоперационных осложнений. В независимых группах пациентов с использованием сравниваемых хирургических вмешательств произведена точная качественная и количественная оценка послеоперационных осложнений: нетромботических - кардиальных, пульмональных, ренальных и тромботических - тромбозов глубоких вен и тромбозов браншей протеза. После реализации исследования было установлено, что замена «классических» операций на «альтернативные» достоверно приводит к принципиальному снижению уровня наиболее жизнеопасных осложнений - кардиальных (острых форм ишемической болезни сердца, нарушений сердечного ритма), пульмональных (пневмоний, тромбоэмболии легочной артерии, респираторного дистресс-синдрома взрослых) и ренальных (острой почечной недостаточности). Некоторое исключение составили менее жизнеопасные тромботические осложнения. Полученные результаты имеют высокий уровень статистической значимости, что позволяет рекомендовать их к рассмотрению к использованию в практике сосудистой хирургии The article presents data from an original study to improve the surgical treatment of abdominal aortic aneurysms. For this purpose, a comparative analysis of two alternate operations was performed: 1) aneurysm resection followed by aortic prosthetics; 2) aortic endoprosthetics. The scientific hypothesis is formulated that the replacement of the «classical» operations of resection of the aneurysm with «alternative» operations of endoprosthetics will lead to a fundamental decrease in the level of postoperative complications. In independent groups of patients using the compared surgical interventions, an accurate qualitative and quantitative assessment of postoperative complications was made: non-thrombotic - cardiac, pulmonary, renal and thrombotic - deep vein thrombosis and prosthetic jaw thrombosis. After the study was completed, it was found that the fundamental replacement of «classical» operations with «alternative» reliably leads to a fundamental decrease in the level of the most life-threatening complications - cardiac (acute forms of coronary heart disease, cardiac arrhythmias), pulmonary (pneumonia, pulmonary thromboembolism, respiratory distress syndrome of adults) and renal (acute renal failure). Some exceptions were less life-threatening thrombotic complications. The results obtained have a high level of statistical significance, which allows us to recommend them for consideration in the practice of vascular surgery

Nonosmotic release of vasopressin and renal aquaporins in impaired urinary dilution in hypothyroidism

2005 ◽  
Vol 289 (4) ◽  
pp. F672-F678 ◽  
Author(s):  
Yung-Chang Chen ◽  
Melissa A. Cadnapaphornchai ◽  
Jianhui Yang ◽  
Sandra N. Summer ◽  
Sandor Falk ◽  
...  
Keyword(s):  
Protein Expression ◽  
Renal Cortex ◽  
Free Water ◽  
Urine Osmolality ◽  
Protein Abundance ◽  
Oral Gavage ◽  
Water Excretion ◽  
Urinary Osmolality ◽  
Water Load ◽  
Fluid Delivery

The purpose of this study was to examine protein expression of renal aquaporins (AQP) and ion transporters in hypothyroid (HT) rats in response to an oral water load compared with controls (CTL) and HT rats replaced with l-thyroxine (HT+T). Hypothyroidism was induced by aminotriazole administration for 10 wk. Body weight, water intake, urine output, solute and urea excretion, and serum and urine osmolality were comparable among the three groups at the conclusion of the 10-wk treatment period. One hour after oral gavage of water (50 ml/kg body wt), HT rats demonstrated significantly less water excretion, higher minimal urinary osmolality, and decreased serum osmolality compared with CTL and HT+T rats. Despite the hyposmolality, plasma vasopressin concentration was elevated in HT rats. These findings in HT rats were associated with an increase in protein abundance of renal cortex AQP1 and inner medulla AQP2. AQP3, AQP4, and the Na-K-2Cl cotransporter were also increased. Moreover, 1 h following the oral water load, HT rats demonstrated a significant increase in the membrane-to-vesicle fraction of AQP2 by Western blot analysis. The defect in urinary dilution in HT rats was reversed by the V2 vasopressin antagonist OPC-31260. In conclusion, impaired urinary dilution in HT rats is primarily compatible with the nonosmotic release of vasopressin and increased protein expression of renal AQP2. The impairment of maximal solute-free water excretion in HT rats, however, appears also to involve diminished distal fluid delivery.

scholarly journals Protein Expression of Mesenchymal Stem Cells after Transfection of pcDNA3.1−-hVEGF165by Ultrasound-Targeted Microbubble Destruction

2011 ◽  
Vol 2011 ◽  
pp. 1-4 ◽  
Author(s):  
Zhaoxia Pu ◽  
Xiangdong You ◽  
Qiyuan Xu ◽  
Feng Gao ◽  
Xiaojie Xie ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Protein Expression ◽  
Specific Gene ◽  
Elisa Kit ◽  
The Third ◽  
Marrow Mesenchymal Stem Cells ◽  
Organ Specific ◽  
A New Technique

Ultrasound-targeted microbubble destruction (UTMD) has been proposed as a new technique for organ-specific gene transfer and drug delivery. This study was performed to investigate the effect of UTMD on marrow mesenchymal stem cells (MSCs) transfected with pcDNA3.1−-hVEGF165.pcDNA3.1−-hVEGF165were transfected into the third passage of MSCs, with or without UTMD under different ultrasound conditions. Protein expression was quantified by hVEGF165-ELISA kit after transfection for 24, 48, and 72 hours. UTMD-mediated transfection of MSCs yielded a significant protein expression. UTMD of mechanic index (MI) 0.6 for 90 seconds led to the highest level of protein expression.

scholarly journals C60 Fullerene Prevents Restraint Stress-Induced Oxidative Disorders in Rat Tissues: Possible Involvement of the Nrf2/ARE-Antioxidant Pathway

2018 ◽  
Vol 2018 ◽  
pp. 1-17 ◽  
Author(s):  
Olga O. Gonchar ◽  
Andriy V. Maznychenko ◽  
Nataliya V. Bulgakova ◽  
Inna V. Vereshchaka ◽  
Tomasz Tomiak ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Lipid Peroxidation ◽  
Protein Expression ◽  
Restraint Stress ◽  
Stress Condition ◽  
Rat Tissues ◽  
Stress Exposure ◽  
The Brain ◽  
Nrf2 Protein

The effects of C60FAS (50 and 500 μg/kg) supplementation, in a normal physiological state and after restraint stress exposure, on prooxidant/antioxidant balance in rat tissues were explored and compared with the effects of the known exogenous antioxidant N-acetylcysteine. Oxidative stress biomarkers (ROS, O2⋅−, H2O2, and lipid peroxidation) and indices of antioxidant status (MnSOD, catalase, GPx, GST, γ-GCL, GR activities, and GSH level) were measured in the brain and the heart. In addition, protein expression of Nrf2 in the nuclear and cytosol fractions as well as the protein level of antiradical enzyme MnSOD and GSH-related enzymes γ-GCLC, GPx, and GSTP as downstream targets of Nrf2 was evaluated by western blot analysis. Under a stress condition, C60FAS attenuates ROS generation and O2⋅− and H2O2 releases and thus decreases lipid peroxidation as well as increases rat tissue antioxidant capacity. We have shown that C60FAS supplementation has dose-dependent and tissue-specific effects. C60FAS strengthened the antiradical defense through the upregulation of MnSOD in brain cells and maintained MnSOD protein content at the control level in the myocardium. Moreover, C60FAS enhanced the GSH level and the activity/protein expression of GSH-related enzymes. Correlation of these changes with Nrf2 protein content suggests that under stress exposure, along with other mechanisms, the Nrf2/ARE-antioxidant pathway may be involved in regulation of glutathione homeostasis. In our study, in an in vivo model, when C60FAS (50 and 500 μg/kg) was applied alone, no significant changes in Nrf2 protein expression as well as in activity/protein levels of MnSOD and GSH-related enzymes in both tissues types were observed. All these facts allow us to assume that in the in vivo model, C60FAS affects on the brain and heart endogenous antioxidative statuses only during the oxidative stress condition.

Expression of vascular permeability factor/vascular endothelial growth factor in normal rat tissues

1993 ◽  
Vol 264 (4) ◽  
pp. C995-C1002 ◽  
Author(s):  
W. T. Monacci ◽  
M. J. Merrill ◽  
E. H. Oldfield
Keyword(s):  
Vascular Endothelial Growth Factor ◽  
In Situ Hybridization ◽  
Rat Tissues ◽  
Vascular Endothelial ◽  
Vascular Permeability Factor ◽  
Organ Specific ◽  
Normal Rat ◽  
Endothelial Growth Factor ◽  
The Brain

Vascular permeability factor (VPF)/vascular endothelial growth factor (VEGF) is a approximately 43-kDa secreted protein that has been shown in bioassays to induce endothelial proliferation, angiogenesis, and capillary hyperpermeability. VPF has been suggested to play an important role in the physiology of normal vasculature. To further elucidate the natural functions of VPF in vivo, the expression of VPF in normal tissues was examined using Northern blot analysis and in situ hybridization histochemistry. VPF mRNA is expressed in the brain, kidney, liver, lung, and spleen of the healthy adult rat. On Northern blots, the relative abundance of VPF mRNA observed in these tissues was highest in the lung and lowest in the spleen. As determined by in situ hybridization, the patterns of VPF expression are organ specific. Hybridization of an antisense VPF probe was concentrated in the cerebellar granule cell layer of the brain and in the glomeruli and tubules of the kidney. In the liver and lung, intense hybridization was observed homogeneously throughout both tissues, demonstrating that VPF mRNA is present in virtually every hepatocyte and pulmonary alveolar cell. Hybridization to the spleen was weaker and more diffuse. The widespread expression and organ-specific distribution of VPF mRNA in normal rat tissues supports the suggestion of an extensive role for this factor in the physiology of normal vasculature.

SNARE protein expression in synaptic terminals and astrocytes in the adult hippocampus: A comparative analysis

Glia ◽  
2011 ◽  
Vol 59 (10) ◽  
pp. 1472-1488 ◽  
Author(s):  
Vanessa Schubert ◽  
David Bouvier ◽  
Andrea Volterra
Keyword(s):  
Comparative Analysis ◽  
Protein Expression ◽  
Snare Protein ◽  
Synaptic Terminals ◽  
Adult Hippocampus

scholarly journals Proteomic Analysis of Capacitated and Non-Capacitated Spermatozoa of Yanbian Yellow Cattle

2020 ◽  
Author(s):  
Xuan Chen ◽  
Zuochen Li ◽  
Yanqiu Lv ◽  
Yichao Xu ◽  
Mimi Cheng ◽  
...  
Keyword(s):  
Protein Transport ◽  
Expression Level ◽  
Molecular Processes ◽  
Proteomics Data ◽  
Pathway Enrichment ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
Yellow Cattle ◽  
Specific Proteins ◽  
The Difference

Abstract Background: Sperm capacitation is a process which occurs prior to fertilization, and is essential for producing high-quality living embryos. The main purpose of this study was to explore the difference of proteomics between capacitated and non-capacitated sperm of Yanbian yellow cattle. Bioinformatic analyses of LC-MS/MS data included GO enrichment, KEGG pathway enrichment, and protein-protein interaction (PPI) analysis. Results: The results revealed 23 specific proteins in the capacitated group and 345 in the non-capacitated group. Compared with non-capacitated sperm, capacitated sperm exhibited 89 upregulated proteins and 509 downregulated proteins. Western blotting was used to confirm our proteomics data. The expression level of PSMD1 in the capacitated sperm group was significantly lower than that in the non-capacitated sperm group, and the expression level of HSPA5 was significantly higher than in the non-capacitated sperm group. Conclusions: Our results revealed that many proteins were differentially expressed between capacitated and non-capacitated sperm, particularly those involved in the proteasome signaling and protein transport signaling pathways. This work enhances our understanding of molecular processes involved in sperm viability in Yanbian yellow cattle, and provides a framework for future studies.

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