scholarly journals Quantitative Proteomic Profiling of Marine Diatom Skeletonema dohrnii in Response to Temperature and Silicate Induced Environmental Stress

2021 ◽  
Vol 11 ◽  
Author(s):  
Satheeswaran Thangaraj ◽  
Satheesh Kumar Palanisamy ◽  
Guicheng Zhang ◽  
Jun Sun
Keyword(s):  
Pathway Analysis ◽  
Environmental Conditions ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Marine Phytoplankton ◽  
Marine Diatom ◽  
Biological Information ◽  
Proteomic Profiling ◽  
Protein Ratio ◽  
Oxidoreductase Activity

Global warming is expected to reduce the nutrient concentration in the upper ocean and affect the physiology of marine diatoms, but the underlying molecular mechanisms controlling these physiological changes are currently unknown. To understand these mechanisms, here we investigated iTRAQ based proteomic profiling of diatom Skeletonema dohrnii in a multifactorial experimental with a combining change of temperature and silicate concentrations. In total, 3369 differently abundant proteins were detected in four different environmental conditions, and the function of all proteins was identified using Gene Ontology and KEGG pathway analysis. For discriminating the proteome variation among samples, multivariate statistical analysis (PCA, PLS-DA) was performed by comparing the protein ratio differences. Further, performing pathway analysis on diatom proteomes, we here demonstrated downregulation of photosynthesis, carbon metabolism, and ribosome biogenesis in the cellular process that leads to decrease the oxidoreductase activity and affects the cell cycle of the diatom. Using PLS-DA VIP score plot analysis, we identified 15 protein biomarkers for discriminating studied samples. Of these, five proteins or gene (rbcL, PRK, atpB, DNA-binding, and signal transduction) identified as key biomarkers, induced by temperature and silicate stress in diatom metabolism. Our results show that proteomic finger-printing of S. dohrnii with different environmental conditions adds biological information that strengthens marine phytoplankton proteome analysis.

scholarly journals Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 308
Author(s):  
Marion Buffard ◽  
Aurélien Naldi ◽  
Gilles Freiss ◽  
Marcel Deckert ◽  
Ovidiu Radulescu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tumor Suppressor ◽  
Signaling Pathways ◽  
Burkitt Lymphoma ◽  
Molecular Mechanisms ◽  
Signal Propagation ◽  
Tumor Formation ◽  
Tissue Type ◽  
Signaling Networks ◽  
Proteomic Profiling

Spleen tyrosine kinase (SYK) can behave as an oncogene or a tumor suppressor, depending on the cell and tissue type. As pharmacological SYK inhibitors are currently evaluated in clinical trials, it is important to gain more information on the molecular mechanisms underpinning these opposite roles. To this aim, we reconstructed and compared its signaling networks using phosphoproteomic data from breast cancer and Burkitt lymphoma cell lines where SYK behaves as a tumor suppressor and promoter. Bioinformatic analyses allowed for unveiling the main differences in signaling pathways, network topology and signal propagation from SYK to its potential effectors. In breast cancer cells, the SYK target-enriched signaling pathways included intercellular adhesion and Hippo signaling components that are often linked to tumor suppression. In Burkitt lymphoma cells, the SYK target-enriched signaling pathways included molecules that could play a role in SYK pro-oncogenic function in B-cell lymphomas. Several protein interactions were profoundly rewired in the breast cancer network compared with the Burkitt lymphoma network. These data demonstrate that proteomic profiling combined with mathematical network modeling allows untangling complex pathway interplays and revealing difficult to discern interactions among the SYK pathways that positively and negatively affect tumor formation and progression.

scholarly journals Feeding a Saccharomyces cerevisiae fermentation product improves udder health and immune response to a Streptococcus uberis mastitis challenge in mid-lactation dairy cows

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
M. Vailati-Riboni ◽  
D. N. Coleman ◽  
V. Lopreiato ◽  
A. Alharthi ◽  
R. E. Bucktrout ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Somatic Cell ◽  
Pathway Analysis ◽  
Molecular Mechanisms ◽  
Somatic Cell Score ◽  
Molecular Networks ◽  
Epithelial Tissue ◽  
Udder Health ◽  
Streptococcus Uberis ◽  
Fermentation Product

Abstract Background We aimed to characterize the protective effects and the molecular mechanisms of action of a Saccharomyces cerevisiae fermentation product (NTK) in response to a mastitis challenge. Eighteen mid-lactation multiparous Holstein cows (n = 9/group) were fed the control diet (CON) or CON supplemented with 19 g/d NTK for 45 d (phase 1, P1) and then infected in the right rear quarter with 2500 CFU of Streptococcus uberis (phase 2, P2). After 36-h, mammary gland and liver biopsies were collected and antibiotic treatment started until the end of P2 (9 d post challenge). Cows were then followed until day 75 (phase 3, P3). Milk yield (MY) and dry matter intake (DMI) were recorded daily. Milk samples for somatic cell score were collected, and rectal and udder temperature, heart and respiration rate were recorded during the challenge period (P2) together with blood samples for metabolite and immune function analyses. Data were analyzed by phase using the PROC MIXED procedure in SAS. Biopsies were used for transcriptomic analysis via RNA-sequencing, followed by pathway analysis. Results DMI and MY were not affected by diet in P1, but an interaction with time was recorded in P2 indicating a better recovery from the challenge in NTK compared with CON. NTK reduced rectal temperature, somatic cell score, and temperature of the infected quarter during the challenge. Transcriptome data supported these findings, as NTK supplementation upregulated mammary genes related to immune cell antibacterial function (e.g., CATHL4, NOS2), epithelial tissue protection (e.g. IL17C), and anti-inflammatory activity (e.g., ATF3, BAG3, IER3, G-CSF, GRO1, ZFAND2A). Pathway analysis indicated upregulation of tumor necrosis factor α, heat shock protein response, and p21 related pathways in the response to mastitis in NTK cows. Other pathways for detoxification and cytoprotection functions along with the tight junction pathway were also upregulated in NTK-fed cows. Conclusions Overall, results highlighted molecular networks involved in the protective effect of NTK prophylactic supplementation on udder health during a subclinical mastitic event.

scholarly journals Proteomic Profiling Reveals the Molecular Changes of Insomnia Patients

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Guanying Wang ◽  
Xiaojuan Ren ◽  
Xingping Zhang ◽  
Qingquan Wang ◽  
Tao Liu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Cholesterol Metabolism ◽  
Sleep Onset ◽  
Public Health Problem ◽  
Sleep Time ◽  
Control Group ◽  
Proteomic Profiling ◽  
Ppi Network ◽  
Metabolic Systems ◽  
Hub Proteins

Background. Insomnia is an economic burden and public health problem. This study is aimed at exploring potential biological pathways and protein networks for insomnia characterized by wakefulness after sleep. Method. Proteomics analysis was performed in the insomnia group with wakefulness and the control group. The differentially expressed proteins (DEPs) were enriched; then, hub proteins were identified by protein-protein interaction (PPI) network and verified by parallel reaction monitoring (PRM). Results. Compared with the control group, the sleep time and efficiency of insomnia patients were decreased, and awakening time and numbers after sleep onset were significantly increased ( P < 0.001 ). The results of proteomic sequencing found 68 DEPs in serum under 1.2-fold changed standard. These DEPs were significantly enriched in humoral immune response, complement and coagulation cascades, and cholesterol metabolism. Through the PPI network, we identified 10 proteins with the highest connectivity as hub proteins. Among them, the differential expression of 9 proteins was verified by PRM. Conclusion. We identified the hub proteins and molecular mechanisms of insomnia patients characterized by wakefulness after sleep. It provided potential molecular targets for the clinical diagnosis and treatment of these patients and indicated that the immune and metabolic systems may be closely related to insomnia characterized by wakefulness after sleep.

scholarly journals Elucidating the Mechanisms of Hugan Buzure Granule in the Treatment of Liver Fibrosis via Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Yi Zhu ◽  
Ming Qiao ◽  
Jianhua Yang ◽  
Junping Hu
Keyword(s):  
Liver Fibrosis ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Docking Simulation ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Transcription Activator ◽  
Active Ingredients ◽  
Oxidoreductase Activity

Objective. To holistically explore the latent active ingredients, targets, and related mechanisms of Hugan buzure granule (HBG) in the treatment of liver fibrosis (LF) via network pharmacology. Methods. First, we collected the ingredients of HBG by referring the TCMSP server and literature and filtered the active ingredients though the criteria of oral bioavailability ≥30% and drug-likeness index ≥0.18. Second, herb-associated targets were predicted and screened based on the BATMAN-TCM and SwissTargetPrediction platforms. Candidate targets related to LF were collected from the GeneCards and OMIM databases. Furthermore, the overlapping target genes were used to construct the protein-protein interaction network and “drug-compound-target-disease” network. Third, GO and KEGG pathway analyses were carried out to illustrate the latent mechanisms of HBG in the treatment of LF. Finally, the combining activities of hub targets with active ingredients were further verified based on software AutoDock Vina. Results. A total of 25 active ingredients and 115 overlapping target genes of HBG and LF were collected. Besides, GO enrichment analysis exhibited that the overlapping target genes were involved in DNA-binding transcription activator activity, RNA polymerase II-specific, and oxidoreductase activity. Simultaneously, the key molecular mechanisms of HBG against LF were mainly involved in PI3K-AKT, MAPK, HIF-1, and NF-κB signaling pathways. Also, molecular docking simulation demonstrated that the key targets of HBG for antiliver fibrosis were IL6, CASP3, EGFR, VEGF, and MAPK. Conclusion. This work validated and predicted the underlying mechanisms of multicomponent and multitarget about HBG in treating LF and provided a scientific foundation for further research.

O579 PROTEOMIC PROFILING AND PATHWAY ANALYSIS: A COMBINED ETIOLOGY-SPECIFIC APPROACH TO UNDERSTANDING PRETERM LABOR

2012 ◽  
Vol 119 ◽  
pp. S465-S465
Author(s):  
L.M. Rodrigues Pereira ◽  
A.P. Reddy ◽  
M.G. Gravett ◽  
J. Hitti ◽  
D. Eschenbach ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Preterm Labor ◽  
Proteomic Profiling ◽  
Specific Approach

scholarly journals Diquat Determines a Deregulation of lncRNA and mRNA Expression in the Liver of Postweaned Piglets

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Jin Wang ◽  
Zhi-xin Li ◽  
Dan-dan Yang ◽  
Pei-qi Liu ◽  
Zhi-qiang Wang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Growth Performance ◽  
Signaling Pathways ◽  
Molecular Mechanisms ◽  
Reduction Process ◽  
Future Research ◽  
Control Group ◽  
Oxidoreductase Activity ◽  
Go Terms ◽  
Porcine Hepatocytes

Oxidative stress is detrimental to animals and can depress the growth performance and regulate the gene expression of animals. However, it remains unclear how oxidative stress regulates the expression of long noncoding RNAs (lncRNAs) and mRNAs. Therefore, the purpose of this article was to explore the profiles of lncRNAs and mRNAs in the liver of piglets under oxidative stress. Here, we constructed a piglet oxidative stress model induced by diquat and evaluated the effects of oxidative stress on the growth performance and antioxidant enzyme activity of piglets. We also used RNA-Seq to examine the global expression of lncRNAs and mRNAs in piglets under oxidative stress. The targets of lncRNAs and mRNAs were enriched in gene ontology (GO) terms and signaling pathways. The results show that the growth performance and activities of antioxidant enzymes were decreased in piglets under oxidative stress. Moreover, eight lncRNAs (6 upregulated and 2 downregulated) and 30 mRNAs (8 upregulated and 22 downregulated) were differentially expressed in the oxidative stress group of piglets compared to the negative control group. According to biological processes in enriched GO terms, the oxoacid metabolic process, intramolecular oxidoreductase activity, and oxidation-reduction process play important roles in oxidative stress. Pathway analysis showed that the signaling pathways involved in insulin and glucose metabolism had a close relationship with oxidative stress. Furtherin vitroexperiments showed that the expression of the upregulated geneGNMTwas significantly increased in primary porcine hepatocytes after diquat stimulation. In contrast, the level of the downregulated geneGCKwas significantly decreased at 12 h in primary porcine hepatocytes after diquat stimulation. Our results expand our knowledge of the lncRNAs and mRNAs transcribed in the livers of piglets under oxidative stress and provide a basis for future research on the molecular mechanisms mediating oxidative stress and tissue damage.

scholarly journals NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica

2019 ◽  
Vol 116 (33) ◽  
pp. 16448-16453 ◽  
Author(s):  
Julia M. Diaz ◽  
Sydney Plummer ◽  
Colleen M. Hansel ◽  
Peter F. Andeer ◽  
Mak A. Saito ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Cell Types ◽  
Redox Balance ◽  
Superoxide Production ◽  
Marine Phytoplankton ◽  
Marine Diatom ◽  
High Sequence Similarity ◽  
Whole Cells ◽  
Wide Range ◽  
Diphenylene Iodonium

Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.

scholarly journals An animal model study on the gene expression profile of meniscal degeneration

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yehan Fang ◽  
Hui Huang ◽  
Gang Zhou ◽  
Qinghua Wang ◽  
Feng Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathway Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Control Group ◽  
Ion Binding ◽  
Endoplasmic Reticulum Membrane ◽  
Rt Pcr ◽  
Go Analysis ◽  
Meniscal Degeneration

AbstractMeniscal degeneration is a very common condition in elderly individuals, but the underlying mechanisms of its occurrence are not completely clear. This study examines the molecular mechanisms of meniscal degeneration. The anterior cruciate ligament (ACL) and lateral collateral ligament (LCL) of the right rear limbs of seven Wuzhishan mini-pigs were resected (meniscal degeneration group), and the left rear legs were sham-operated (control group). After 6 months, samples were taken for gene chip analysis, including differentially expressed gene (DEG) analysis, gene ontology (GO) analysis, clustering analysis, and pathway analysis. The selected 12 DEGs were validated by real time reverse transcription-polymerase chain reaction (RT-PCR). The two groups showed specific and highly clustered DEGs. A total of 893 DEGs were found, in which 537 are upregulated, and 356 are downregulated. The GO analysis showed that the significantly affected biological processes include nitric oxide metabolic process, male sex differentiation, and mesenchymal morphogenesis, the significantly affected cellular components include the endoplasmic reticulum membrane, and the significantly affected molecular functions include transition metal ion binding and iron ion binding. The pathway analysis showed that the significantly affected pathways include type II diabetes mellitus, inflammatory mediator regulation of TRP channels, and AMPK signaling pathway. The results of RT-PCR indicate that the microarray data accurately reflects the gene expression patterns. These findings indicate that several molecular mechanisms are involved in the development of meniscal degeneration, thus improving our understanding of meniscal degeneration and provide molecular therapeutic targets in the future.

scholarly journals Functional Proteomic Analysis of Human Nucleolus

2002 ◽  
Vol 13 (11) ◽  
pp. 4100-4109 ◽  
Author(s):  
Alexander Scherl ◽  
Yohann Couté ◽  
Catherine Déon ◽  
Aleth Callé ◽  
Karine Kindbeiter ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Convincing Evidence ◽  
Biological Processes ◽  
Functional Classification ◽  
Control Of Gene Expression ◽  
Nucleolar Proteins ◽  
Nuclear Domain

The notion of a “plurifunctional” nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of ∼350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes.

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