共查询到20条相似文献,搜索用时 31 毫秒
1.
Annett Markus-Koch Oliver Schmitt Susanne Seemann Jan Lukas Dirk Koczan Mathias Ernst Georg Fuellen Andreas Wree Arndt Rolfs Jiankai Luo 《Cellular & molecular biology letters》2017,22(1):16
Background
ADAM23 is widely expressed in the embryonic central nervous system and plays an important role in tissue formation.Results
In this study, we showed that ADAM23 contributes to cell survival and is involved in neuronal differentiation during the differentiation of human neural progenitor cells (hNPCs). Upregulation of ADAM23 in hNPCs was found to increase the number of neurons and the length of neurite, while its downregulation decreases them and triggers cell apoptosis. RNA microarray analysis revealed mechanistic insights into genes and pathways that may become involved in multiple cellular processes upon up- or downregulation of ADAM23.Conclusions
Our results suggest that ADAM23 regulates neuronal differentiation by triggering specific signaling pathways during hNPC differentiation.2.
Xue-Gang Xu Lin Gong Tian-Ling Jiang Yuan-Hong Li Xing-Hua Gao Haishan Tian Hong-Duo Chen 《Biotechnology letters》2018,40(6):1009-1014
Objectives
To explore potential effects of recombinant human fibroblast growth factor 20 (rhFGF20) in the growth of cultured mouse vibrissal follicles.Results
The growth of cultured mouse vibrissal follicles was significantly induced by rhFGF20 in a dose dependent pattern in the in vitro vibrissal follicle organ culture model. However, too high concentration of rhFGF20 could inhibit the growth of vibrissal follicles. We further demonstrated that rhFGF20 stimulated the proliferation of hair matrix cells and activated Wnt/β-catenin signaling pathway.Conclusions
The rhFGF20 might be a potential therapeutic agent to treat hair loss disorders.3.
Patrycja?Podlaszczuk Maciej?Kamiński Rados?aw?W?odarczyk Krzysztof?Kaczmarek Tomasz?Janiszewski Piotr?Minias
Background
Moult is one of the most costly activities in the annual cycle of birds and most avian species separate moult from other energy-demanding activities, such as migration. To this end, young birds tend to undergo the first post-juvenile moult before the onset of migration, but in some species the time window for the pre-migratory feather replacement is too narrow. We hypothesized that in such species an increased investment in the structural quality of juvenile feathers may allow to retain juvenile plumage throughout the entire migratory period and delay moult until arriving at wintering grounds, thus avoiding a moult-migration overlap.Methods
The effect of juvenile plumage quality on the occurrence of moult-migration overlap was studied in a migratory shorebird, the common snipe Gallinago gallinago. Ca. 400 of first-year common snipe were captured during their final stage of autumn migration through Central Europe. The quality of juvenile feathers was assessed as the mass-length residuals of retained juvenile rectrices. Condition of migrating birds was assessed with the mass of accumulated fat reserves and whole-blood hemoglobin concentration. Path analysis was used to disentangle complex interrelationships between plumage quality, moult and body condition.Results
Snipe which grew higher-quality feathers in the pre-fledging period were less likely to initiate moult during migration. Individuals moulting during migration had lower fat loads and hemoglobin concentrations compared to non-moulting birds, suggesting a trade-off in resource allocation, where energetic costs of moult reduced both energy reserves available for migration and resources available for maintenance of high oxygen capacity of blood.Conclusions
The results of this study indicate that a major life-history trade-off in a migratory bird may be mediated by the quality of juvenile plumage. This is consistent with a silver spoon effect, where early-life investment in feather quality affects future performance of birds during migration period. Our results strongly suggest that the juvenile plumage, although retained for a relatively short period of time, may have profound consequences for individuals’ fitness.4.
Background
MicroRNAs (miRNAs) regulate many biological processes by post-translational gene silencing. Analysis of miRNA expression profiles is a reliable method for investigating particular biological processes due to the stability of miRNA and the development of advanced sequencing methods. However, this approach is limited by the broad specificity of miRNAs, which may target several mRNAs.Result
In this study, we developed a method for comprehensive annotation of miRNA array or deep sequencing data for investigation of cellular biological effects. Using this method, the specific pathways and biological processes involved in Alzheimer’s disease were predicted with high correlation in four independent samples. Furthermore, this method was validated for evaluation of cadmium telluride (CdTe) nanomaterial cytotoxicity. As a result, apoptosis pathways were selected as the top pathways associated with CdTe nanoparticle exposure, which is consistent with previous studies.Conclusions
Our findings contribute to the validation of miRNA microarray or deep sequencing results for early diagnosis of disease and evaluation of the biological safety of new materials and drugs.5.
Background
Clinical statement alone is not enough to predict the progression of disease. Instead, the gene expression profiles have been widely used to forecast clinical outcomes. Many genes related to survival have been identified, and recently miRNA expression signatures predicting patient survival have been also investigated for several cancers. However, miRNAs and their target genes associated with clinical outcomes have remained largely unexplored.Methods
Here, we demonstrate a survival analysis based on the regulatory relationships of miRNAs and their target genes. The patient survivals for the two major cancers, ovarian cancer and glioblastoma multiforme (GBM), are investigated through the integrated analysis of miRNA-mRNA interaction pairs.Results
We found that there is a larger survival difference between two patient groups with an inversely correlated expression profile of miRNA and mRNA. It supports the idea that signatures of miRNAs and their targets related to cancer progression can be detected via this approach.Conclusions
This integrated analysis can help to discover coordinated expression signatures of miRNAs and their target mRNAs that can be employed for therapeutics in human cancers.6.
Jinguo Liu Lin Yu Cuicui Chen Jian Zhou Xin Gong Dandan Li Dongni Hou Yuanlin Song Changzhou Shao 《Mycopathologia》2018,183(2):337-348
Background
C-type lectin receptors (CLRs), Toll-like receptors (TLRs), and Nod-like receptors (NLRs) have the ability to recognize Aspergillus fumigatus (A. fumigates) and induce innate immune response. Dectin-1 is a well-described CLR, while interleukin-1 receptor-associated kinase 1 (Irak1) and receptor-interacting protein 2 (Rip2) are pivotal adaptor proteins of TLRs and NLRs signaling pathways, respectively.Objectives
Our primary aim is to elucidate whether Dectin-1 regulates the expression of Irak1 and Rip2, and confirm that CLRs, TLRs, and NLRs pathways act synergistically in response to A. fumigatus infection.Methods
Pulmonary infection mouse models were established. Myeloid cells were differentiated in cell culture and examined by inverted microscopy, flow cytometry, and scanning electron microscopy. The relative mRNA levels were determined by qRT-PCR. The protein expression levels were determined by immunohistochemistry and Western blot.Results
The expression of Dectin-1, Irak1, Rip2, and phosphorylation level of nuclear factor (NF)-κB p65 were induced by conidia in immunocompetent mice, while their expression and phosphorylation level were inhibited in immunocompromised mice after the administration of conidia. Conidia increased the expression of Dectin-1, Irak1, and Rip2 in myeloid cells, while Dectin-1 silencing significantly reduced their expression.Conclusion
Our findings demonstrate that Dectin-1, Irak1, and Rip2 are involved in response to A. fumigatus infection. Dectin-1 modulates the expression of Irak1 and Rip2. Additionally, these three signaling pathways are interconnected, and CLRs pathway plays a dominant role against A. fumigatus invasion.7.
Fan Zhang Haoting Chen Li Na Zhao Hui Liu Teresa M. Przytycka Jie Zheng 《BMC systems biology》2016,10(Z1):S7
Background
Cellular responses to extracellular perturbations require signaling pathways to capture and transmit the signals. However, the underlying molecular mechanisms of signal transduction are not yet fully understood, thus detailed and comprehensive models may not be available for all the signaling pathways. In particular, insufficient knowledge of parameters, which is a long-standing hindrance for quantitative kinetic modeling necessitates the use of parameter-free methods for modeling and simulation to capture dynamic properties of signaling pathways.Results
We present a computational model that is able to simulate the graded responses to degradations, the sigmoidal biological relationships between signaling molecules and the effects of scheduled perturbations to the cells. The simulation results are validated using experimental data of protein phosphorylation, demonstrating that the proposed model is capable of capturing the main trend of protein activities during the process of signal transduction. Compared with existing simulators, our model has better performance on predicting the state transitions of signaling networks.Conclusion
The proposed simulation tool provides a valuable resource for modeling cellular signaling pathways using a knowledge-based method.8.
Andrew Brandmaier Sheng-Qi Hou Sandra Demaria Silvia C. Formenti Wen H. Shen 《生物学前沿》2017,12(3):163-174
Background
PTEN is well known to function as a tumor suppressor that antagonizes oncogenic signaling and maintains genomic stability. The PTEN gene is frequently deleted or mutated in human cancers and the wide cancer spectrum associated with PTEN deficiency has been recapitulated in a variety of mouse models of Pten deletion or mutation. Pten mutations are highly penetrant in causing various types of spontaneous tumors that often exhibit resistance to anticancer therapies including immunotherapy. Recent studies demonstrate that PTEN also regulates immune functionality.Objective
To understand the multifaceted functions of PTEN as both a tumor suppressor and an immune regulator.Methods
This review will summarize the emerging knowledge of PTEN function in cancer immunoediting. In addition, the mechanisms underlying functional integration of various PTEN pathways in regulating cancer evolution and tumor immunity will be highlighted.Results
Recent preclinical and clinical studies revealed the essential role of PTEN in maintaining immune homeostasis, which significantly expands the repertoire of PTEN functions. Mechanistically, aberrant PTEN signaling alters the interplay between the immune system and tumors, leading to immunosuppression and tumor escape.Conclusion
Rational design of personalized anti-cancer treatment requires mechanistic understanding of diverse PTEN signaling pathways in modulation of the crosstalk between tumor and immune cells.9.
Mohammad Reza Abbaszadegan Anali Riahi Mohammad Mahdi Forghanifard Meysam Moghbeli 《Cellular & molecular biology letters》2018,23(1):42
Background
Esophageal squamous cell carcinoma (ESCC) is the most common histological type of esophageal cancer, with a poor prognosis. Deregulation of WNT and NOTCH signaling pathways is important in ESCC progression, which can be due to either malfunction of their components or crosstalk with other pathways. Therefore, identification of new crosstalk between such pathways may be effective to introduce new strategies for targeted therapy of cancer. A correlation study was performed to assess the probable interaction between growth factor receptors and WNT/NOTCH pathways via the epidermal growth factor receptor (EGFR) and Musashi1 (MSI1), respectively.Methods
Levels of MSI1/EGFR mRNA expression in tumor tissues from 48 ESCC patients were compared to their corresponding normal tissues using real-time polymerase chain reaction.Results
There was a significant correlation between EGFR and MSI1 expression (p?=?0.05). Moreover, there was a significant correlation between EGFR/MSI1 expression and grade of tumor differentiation (p?=?0.02).Conclusion
This study confirms a direct correlation between MSI1 and EGFR and may support the important role of MSI1 in activation of EGFR through NOTCH/WNT pathways in ESCC.10.
Background
MicroRNAs (miRNAs) have been shown to play important roles in regulating gene expression. Since miRNAs are often evolutionarily conserved and their precursors can be folded into stem-loop hairpins, many miRNAs have been predicted. Yet experimental confirmation is difficult since miRNA expression is often specific to particular tissues and developmental stages.Results
Analysis of 29 human and 230 mouse longSAGE libraries revealed the expression of 22 known and 10 predicted mammalian miRNAs. Most were detected in embryonic tissues. Four SAGE tags detected in human embryonic stem cells specifically match a cluster of four human miRNAs (mir-302a, b, c&d) known to be expressed in embryonic stem cells. LongSAGE data also suggest the existence of a mouse homolog of human and rat mir-493.Conclusion
The observation that some orphan longSAGE tags uniquely match miRNA precursors provides information about the expression of some known and predicted miRNAs.11.
Renato de Souza Pinto Lemgruber Kaspar Valgepea Mark P. Hodson Ryan Tappel Sean D. Simpson Michael Köpke Lars K. Nielsen Esteban Marcellin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):35
Introduction
Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.Objective
To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.Methods
Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.Results
Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.Conclusion
Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.12.
Objectives
To improve the potential value of feather, which is a valuable protein resource, we have separated and identified antioxidant peptide(s) from feather hydrolysate.Results
Feather hydrolysate was prepared by fermentation with Bacillus subtilis S1–4. Antioxidative peptides were separated by sequential acid precipitation, cation exchange, and reversed-phase fast performance liquid chromatography. Finally, a peptide with antioxidative activity was identified as Ser-Asn-Leu-Cys-Arg-Pro-Cys-Gly by MALDI time-of-flight (TOF)/TOF analysis, and determined to represent a portion of feather keratin near its N-terminal. A synthesized peptide with the same sequence was used to characterize its antioxidative properties, including scavenging free radicals, reducing power, and Fe2+ chelation. In terms of the peptide’s amino acid composition, the antioxidative activity might be mainly attributed to Cys and other amino acid residues.Conclusion
Feather keratin is a good source for the quantitative preparation of antioxidative peptides.13.
Antonella Del-Corso Mario Cappiello Roberta Moschini Francesco Balestri Umberto Mura 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):2
Introduction
While the evolutionary adaptation of enzymes to their own substrates is a well assessed and rationalized field, how molecules have been originally selected in order to initiate and assemble convenient metabolic pathways is a fascinating, but still debated argument.Objectives
Aim of the present study is to give a rationale for the preferential selection of specific molecules to generate metabolic pathways.Methods
The comparison of structural features of molecules, through an inductive methodological approach, offer a reading key to cautiously propose a determining factor for their metabolic recruitment.Results
Starting with some commonplaces occurring in the structural representation of relevant carbohydrates, such as glucose, fructose and ribose, arguments are presented in associating stable structural determinants of these molecules and their peculiar occurrence in metabolic pathways.Conclusions
Among other possible factors, the reliability of the structural asset of a molecule may be relevant or its selection among structurally and, a priori, functionally similar molecules.14.
Jie Yang Jianhua Cheng Bo Sun Haijing Li Shengming Wu Fangting Dong Xianzhong Yan 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):40
Introduction
Hypoxia commonly occurs in cancers and is highly related with the occurrence, development and metastasis of cancer. Treatment of triple negative breast cancer remains challenge. Knowledge about the metabolic status of triple negative breast cancer cell lines in hypoxia is valuable for the understanding of molecular mechanisms of this tumor subtype to develop effective therapeutics.Objectives
Comprehensively characterize the metabolic profiles of triple negative breast cancer cell line MDA-MB-231 in normoxia and hypoxia and the pathways involved in metabolic changes in hypoxia.Methods
Differences in metabolic profiles affected pathways of MDA-MB-231 cells in normoxia and hypoxia were characterized using GC–MS based untargeted and stable isotope assisted metabolomic techniques.Results
Thirty-three metabolites were significantly changed in hypoxia and nine pathways were involved. Hypoxia increased glycolysis, inhibited TCA cycle, pentose phosphate pathway and pyruvate carboxylation, while increased glutaminolysis in MDA-MB-231 cells.Conclusion
The current results provide metabolic differences of MDA-MB-231 cells in normoxia and hypoxia conditions as well as the involved metabolic pathways, demonstrating the power of combined use of untargeted and stable isotope-assisted metabolomic methods in comprehensive metabolomic analysis.15.
Background
MicroRNAs (miRNAs) are a large class of non-coding RNAs with important functions wide spread in animals, plants and viruses. Studies showed that an RNase III family member called Drosha recognizes most miRNAs, initiates their processing and determines the mature miRNAs. The Drosha processing sites identification will shed some light on both miRNA identification and understanding the mechanism of Drosha processing.Methods
We developed a computational method for Drosha processing site predicting, named as DroshaPSP, which employs a two-layer mathematical model to integrate structure feature in the first layer and sequence features in the second layer. The performance of DroshaPSP was estimated by 5-fold cross-validation and measured by ACC (accuracy), Sn (sensitivity), Sp (specificity), P (precision) and MCC (Matthews correlation coefficient).Results
The results of testing DroshaPSP on the miRNA data of Drosophila melanogaster indicated that the Sn, Sp, and MCC thereof reach to 0.86, 0.99 and 0.86 respectively.Conclusions
We found the Shannon entropy, a chemical kinetics feature, is a significant feature in telling the true sites among the nearby sites and improving the performance.16.
Nadine Strehmel David Strunk Veronika Strehmel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):135
Introduction
Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.Objectives
To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.Methods
The extracted compounds were analyzed by LC/MS and GC/MS.Results
The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.Conclusion
From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.17.
Patrick J. C. Tardivel Cécile Canlet Gaëlle Lefort Marie Tremblay-Franco Laurent Debrauwer Didier Concordet Rémi Servien 《Metabolomics : Official journal of the Metabolomic Society》2017,13(10):109
Introduction
Experiments in metabolomics rely on the identification and quantification of metabolites in complex biological mixtures. This remains one of the major challenges in NMR/mass spectrometry analysis of metabolic profiles. These features are mandatory to make metabolomics asserting a general approach to test a priori formulated hypotheses on the basis of exhaustive metabolome characterization rather than an exploratory tool dealing with unknown metabolic features.Objectives
In this article we propose a method, named ASICS, based on a strong statistical theory that handles automatically the metabolites identification and quantification in proton NMR spectra.Methods
A statistical linear model is built to explain a complex spectrum using a library containing pure metabolite spectra. This model can handle local or global chemical shift variations due to experimental conditions using a warping function. A statistical lasso-type estimator identifies and quantifies the metabolites in the complex spectrum. This estimator shows good statistical properties and handles peak overlapping issues.Results
The performances of the method were investigated on known mixtures (such as synthetic urine) and on plasma datasets from duck and human. Results show noteworthy performances, outperforming current existing methods.Conclusion
ASICS is a completely automated procedure to identify and quantify metabolites in 1H NMR spectra of biological mixtures. It will enable empowering NMR-based metabolomics by quickly and accurately helping experts to obtain metabolic profiles.18.
Raghuveera Kumar Goel Mona Meyer Marta Paczkowska Jüri Reimand Frederick Vizeacoumar Franco Vizeacoumar TuKiet T. Lam Kiven Erique Lukong 《Proteome science》2018,16(1):16
Background
The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolutionarily conserved relative of the Src family kinases (SFKs). Tyrosine kinases are known to regulate a number of cellular processes and pathways via phosphorylating substrate proteins directly and/or by partaking in signaling cross-talks leading to the indirect modulation of various signaling intermediates. In a previous study, we profiled the tyrosine-phosphoproteome of SRMS and identified multiple candidate substrates of the kinase. The broader cellular signaling intermediates of SRMS are unknown.Methods
In order to uncover the broader SRMS-regulated phosphoproteome and identify the SRMS-regulated indirect signaling intermediates, we performed label-free global phosphoproteomics analysis on cells expressing wild-type SRMS. Using computational database searching and bioinformatics analyses we characterized the dataset.Results
Our analyses identified 60 hyperphosphorylated (phosphoserine/phosphothreonine) proteins mapped from 140 hyperphosphorylated peptides. Bioinfomatics analyses identified a number of significantly enriched biological and cellular processes among which DNA repair pathways were found to be upregulated while apoptotic pathways were found to be downregulated. Analyses of motifs derived from the upregulated phosphosites identified Casein kinase 2 alpha (CK2α) as one of the major potential kinases contributing to the SRMS-dependent indirect regulation of signaling intermediates.Conclusions
Overall, our phosphoproteomics analyses identified serine/threonine phosphorylation dynamics as important secondary events of the SRMS-regulated phosphoproteome with implications in the regulation of cellular and biological processes.19.
20.
Kunmei Chen Yongting Yu Kai Sun Heping Xiong Chunming Yu Ping Chen Jikang Chen Gang Gao Aiguo Zhu 《BMC plant biology》2018,18(1):369