scholarly journals In-depth proteomic profiling captures subtype-specific features of craniopharyngiomas

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jung Hee Kim ◽  
Hyeyoon Kim ◽  
Kisoon Dan ◽  
Seong-Ik Kim ◽  
Sung-Hye Park ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Bioinformatics Analysis ◽  
Integrated Approach ◽  
System Level ◽  
Proteomic Profiling ◽  
Neuron Development ◽  
Bioinformatics Analyses ◽  
Epithelial Tumor ◽  
Proteomic Study ◽  
Adamantinomatous Craniopharyngioma

AbstractCraniopharyngiomas are rare epithelial tumors derived from pituitary gland embryonic tissue. This epithelial tumor can be categorized as an adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) subtype with histopathological and genetic differences. Genomic and transcriptomic profiles of craniopharyngiomas have been investigated; however, the proteomic profile has yet to be elucidated and added to these profiles. Recent improvements in high-throughput quantitative proteomic approaches have introduced new opportunities for a better understanding of these diseases and the efficient discovery of biomarkers. We aimed to confirm subtype-associated proteomic changes between ACP and PCP specimens. We performed a system-level proteomic study using an integrated approach that combines mass spectrometry-based quantitative proteomic, statistical, and bioinformatics analyses. The bioinformatics analysis showed that differentially expressed proteins between ACP and PCP were significantly involved in mitochondrial organization, fatty acid metabolic processes, exocytosis, the inflammatory response, the cell cycle, RNA splicing, cell migration, and neuron development. Furthermore, using network analysis, we identified hub proteins that were positively correlated with ACP and PCP phenotypes. Our findings improve our understanding of the pathogenesis of craniopharyngiomas and provide novel insights that may ultimately translate to the development of craniopharyngioma subtype-specific therapeutics.

scholarly journals In-depth Proteomic Profiling Captures Subtype-specific Features of Craniopharyngiomas

2021 ◽  
Author(s):  
Jung Hee Kim ◽  
Hyeyoon Kim ◽  
Kisoon Dan ◽  
Seong-Ik Kim ◽  
Sung-Hye Park ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Bioinformatics Analysis ◽  
Integrated Approach ◽  
System Level ◽  
Differentially Expressed Proteins ◽  
Proteomic Profiling ◽  
Neuron Development ◽  
Epithelial Tumor ◽  
Proteomic Study ◽  
Adamantinomatous Craniopharyngioma

Abstract Purpose: Craniopharyngiomas are rare epithelial tumors derived from pituitary gland embryonic tissue. This epithelial tumor can be categorized as an adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) subtype with histopathological and genetic differences. Genomic and transcriptomic profiles of craniopharyngiomas have been investigated; however, the proteomic profile has yet to be elucidated and added to these profiles. Recent improvements in high-throughput quantitative proteomic approaches have introduced new opportunities for a better understanding of these diseases and the efficient discovery of biomarkers. We aimed to confirm subtype-associated proteomic changes between ACP and PCP specimens.Methods: We performed a system-level proteomic study using an integrated approach that combines mass spectrometry-based quantitative proteomic, statistical, and bioinformatics analyses.Results: The bioinformatics analysis showed that differentially expressed proteins between ACP and PCP were significantly involved in mitochondrial organization, fatty acid metabolic processes, exocytosis, the inflammatory response, the cell cycle, RNA splicing, cell migration, and neuron development. Furthermore, using network analysis, we identified hub proteins that were positively correlated with ACP and PCP phenotypes.Conclusions: Our findings improve our understanding of the pathogenesis of craniopharyngiomas and provide novel insights that may ultimately translate to the development of craniopharyngioma subtype-specific therapeutics.

Common Currency for System Integration of High Intensity Energy Subsystems

2011 ◽  
Author(s):  
David M. Pratt ◽  
David J. Moorhouse
Keyword(s):  
Heat Transfer ◽  
Heat Sink ◽  
High Intensity ◽  
Waste Heat ◽  
Integrated Approach ◽  
High Energy ◽  
Heat Fluxes ◽  
System Level ◽  
Level Energy ◽  
Common Currency

Aerospace vehicle design has progressed in an evolutionary manner, with certain discrete changes such as turbine engines replacing propellers for higher speeds. The evolution has worked very well for commercial aircraft because the major components can be optimized independently. This is not true for many military configurations which require a more integrated approach. In addition, the introduction of aspects for which there is no pre-existing database requires special attention. Examples of subsystem that have no pre-existing data base include directed energy weapons (DEW) such as high power microwaves (HPM) and high energy lasers (HEL). These devices are inefficient, therefore a large portion of the energy required to operate the device is converted to waste heat and must be transferred to a suitable heat sink. For HPM, the average heat load during one ‘shot’ is on the same order as traditional subsystems and thus designing a thermal management system is possible. The challenge is transferring the heat from the HPM device to a heat sink. The power density of each shot could be hundreds of megawatts. This heat must be transferred from the HPM beam dump to a sink. The heat transfer must occur at a rate that will support shots in the 10–100Hz range. For HEL systems, in addition to the high intensity, there are substantial system level thermal loads required to provide an ‘infinite magazine.’ Present models are inadequate to analyze these problems, current systems are unable to sustain the energy dissipation required and the high intensity heat fluxes applied over a very short duration phenomenon is not well understood. These are examples of potential future vehicle integration challenges. This paper addresses these and other subsystems integration challenges using a common currency for vehicle optimization. Exergy, entropy generation minimization, and energy optimization are examples of methodologies that can enable the creation of energy optimized systems. These approaches allow the manipulation of fundamental equations governing thermodynamics, heat transfer, and fluid mechanics to produce minimized irreversibilities at the vehicle, subsystem and device levels using a common currency. Applying these techniques to design for aircraft system-level energy efficiency would identify not only which subsystems are inefficient but also those that are close to their maximum theoretical efficiency while addressing diverse system interaction and optimal subsystem integration. Such analyses would obviously guide researchers and designers to the areas having the highest payoff and enable departures from the evolutionary process and create a breakthrough design.

Diagnosis of thymic epithelial tumor subtypes by a quantitative proteomic approach

The Analyst ◽  
2018 ◽  
Vol 143 (11) ◽  
pp. 2491-2500 ◽  
Author(s):  
Ting Zhao ◽  
Jie Wu ◽  
Xiaohui Liu ◽  
Lei Zhang ◽  
Gang Chen ◽  
...  
Keyword(s):  
Proteomic Profiling ◽  
Epithelial Tumor ◽  
Tumor Subtypes ◽  
Thymic Epithelial Tumor ◽  
Proteomic Approach

This study shows the first depth proteomic profiling of all TET subtypes and six candidate biomarkers were identified and validated.

scholarly journals Bioinformatics Analysis on DNA Barcode Sequences for Species Identification: A Review

2019 ◽  
pp. 1-12 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Ly Le
Keyword(s):  
Genetic Information ◽  
Bioinformatics Analysis ◽  
Low Cost ◽  
Dna Barcode ◽  
Large Data ◽  
Taxonomic Identification ◽  
Limited Information ◽  
Bioinformatics Analyses ◽  
Dna Library

Classification of organisms is the primary step in management of biodiversity, breeding, conservation and development of populations and distinguishing adulterant objects. There are many approaches in taxonomic identification, from morphological, PCR-based to sequence-based techniques. Molecular methods give more accurate results than morphological comparisons and are independent of plant stages. PCR-based methods are low-cost but their limited information gives less reproducibility and can only distinguish samples among determined groups. In contrast, in sequence-based methods each nucleotide site is considered as genetic information hence a sequence of nucleotide represents large data, which is highly specific and more stable than PCR bands. Establishment of worldwide DNA library for barcoding is essential. There were previous reviews on screenings and applications of barcodes in different taxa. In this review we discussed common bioinformatics analyses as well as some new improved techniques relying on barcoding approaches.

scholarly journals lncRNA MRUL Suppressed Non-Small Cell Lung Cancer Cells Proliferation and Invasion by Targeting miR-17-5p/SRSF2 Axis

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Ying Chen ◽  
Tianle Shen ◽  
Xuping Ding ◽  
Cui Ma ◽  
Lei Cheng ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Rna Splicing ◽  
Bioinformatics Analysis ◽  
Small Cell ◽  
Small Cell Lung ◽  
Splice Site Selection ◽  
Invasion And Migration ◽  
And Migration

The two broad histological subtypes of lung cancer are small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), which are the leading causes of cancer-related death in the world. Long noncoding RNAs (lncRNAs) have been verified to be critical in the regulation of cancer development. The present study identified and elucidated the regulatory roles of a novel lncRNA MRUL in NSCLC. The results showed that MRUL was overexpressed in NSCLC samples and correlated with the poor prognosis of patients who had NSCLC. Moreover, this research has for the first time demonstrated that MRUL acted as an oncogenetic lncRNA in NSCLC. Knockdown of MRUL considerably repressed NSCLC cell proliferation, invasion, and migration. The bioinformatics analysis showed that MRUL was involved in regulating multiple RNA splicing and proliferation-related biological processes, such as mRNA splicing, RNA splicing, mRNA processing, mRNA 3 ′ -end processing, mRNA splice site selection, and DNA replication. By combining bioinformatics analysis and experimental validation, we found that MRUL regulated NSCLC progression through promoting SRSF2 by sponging miR-17 in NSCLC cells. The discoveries indicated that MRUL could be a therapeutic target and a potential diagnostic for NSCLC.

scholarly journals Researching ecosystems in innovation contexts

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Erkko Autio ◽  
Llewellyn D.W. Thomas
Keyword(s):  
Design Methodology ◽  
Integrated Approach ◽  
System Level ◽  
Coherent System ◽  
Innovation Ecosystem ◽  
Comprehensive Overview ◽  
Content Type ◽  
Extant Literature ◽  
Innovation Ecosystems ◽  
Collective Production

PurposeThe rapid adoption of the ecosystem concept in innovation contexts has led to a proliferation of differing uses. Scholars need to be crystal clear which concept of the ecosystem they are using to facilitate communication between scholars and allow for cumulativeness and creativity. This paper aims to introduce some clarity into the conceptual mist that surrounds the notion of “ecosystems” in innovation contexts.Design/methodology/approachA review of the extant literature on ecosystems in innovation contexts to derive an integrated approach to understanding the variety of constructs in use.FindingsThis paper introduces clarity into the conceptual mist that surrounds the term “innovation ecosystem”, showing there are three basic types of ecosystems, all of which have a common focus on the collective production of a coherent system-level output.Originality/valueContributes through a comprehensive overview of the differing ecosystem types in innovation contexts and with a heuristic to disambiguate types of innovation ecosystems.

scholarly journals Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6495 ◽  
Author(s):  
Chao Niu ◽  
Min Jiang ◽  
Na Li ◽  
Jianguo Cao ◽  
Meifang Hou ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Stress Responses ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Marker Genes ◽  
Bioinformatics Analyses ◽  
Soil And Water

Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could help us understand the potential molecular mechanisms or signaling pathways responsive to heavy metal stress in plants, and could be applied as marker genes to track heavy metal pollution in soil and water through detecting their expression in plants growing in those environments.

scholarly journals Integrative analysis of miRNA-mRNA network in high altitude retinopathy by bioinformatics analysis

2021 ◽  
Author(s):  
Tong Su ◽  
Chufeng Gu ◽  
Deji Draga ◽  
Chuandi Zhou ◽  
Thashi Lhamo ◽  
...  
Keyword(s):  
High Altitude ◽  
Bioinformatics Analysis ◽  
Cell Model ◽  
Expression Profiles ◽  
Oxygen Deficiency ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Bioinformatics Analyses ◽  
Effective Prevention ◽  
Qrt Pcr

High-altitude retinopathy (HAR) is an ocular manifestation of acute oxygen deficiency at high altitudes. Although the pathophysiology of HAR has been revealed by many studies in recent years, the molecular mechanism is not yet clear. Our study aimed to systematically identify the genes and miRNA and explore the potential biomarkers associated with HAR by integrated bioinformatics analysis. The mRNA and miRNA expression profiles were obtained from the GEO database. We performed Gene Ontology (GO) functional annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Potential target gene analysis and miRNA-mRNA network analysis were also conducted. Quantitative RT-PCR (qRT-PCR) was used to validate the results of the bioinformatics analysis. Through a series of bioinformatics analyses and experiments, we selected 16 differentially expressed miRNAs (DE-miRNAs) and 157 differentially expressed genes (DEGs) related to AMS and constructed a miRNA-mRNA network containing 240 relationship pairs. The hub genes were filtered from the PPI network: IL7R, FOS, IL10, FCGR2A, DDX3X, CDK1, BCL11B and HNRNPH1, which were all downregulated in the AMS group. Then, 9 upregulated DE-miRNAs and 8 hub genes were verified by qRT-PCR in our hypoxia-induced HAR cell model. The expression of miR-3177-3p, miR-369-3p, miR-603, miR-495, miR-4791, miR-424-5p, FOS, IL10 and IL7R was consistent with our bioinformatics results. In conclusion, FOS, IL10, IL-7R and 7 DE-miRNAs may participate in the development of HAR. Our findings will contribute to the identification of biomarkers and promote the effective prevention and treatment of HAR in the future.

A HYPERRELATIONAL APPROACH TO INTEGRATION AND MANIPULATION OF DATA IN MULTIDATABASE SYSTEMS

1996 ◽  
Vol 05 (04) ◽  
pp. 395-429 ◽  
Author(s):  
CHIANG LEE ◽  
MING-CHUAN WU
Keyword(s):  
Query Language ◽  
Integrated Approach ◽  
System Level ◽  
Mathematical Basis ◽  
Data Manipulation ◽  
Global Database ◽  
The Past ◽  
Query Transformation ◽  
Multidatabase Systems ◽  
The Impact

The issue of interoperability among multiple autonomous databases has attracted a lot of attention from researchers in these years. The past research on this issue can be roughly divided into two main categories: the tightly-integrated approach that integrate databases by building an integrated schema and the loosely-integrated approach that achieves interoperability by using a multidatabase language. Most of the past efforts focused on the issues in the first approach. The problem with the first approach is, however, that it lacks a convenient representation of the integrated schema at the system level and a sound mathematical basis for data manipulation in a multidatabase system. In this paper, we propose to use hyperrelations as a powerful and succinct model for the global level representation of heterogeneous database schemas. A hyperrelation has the structure of a relation, but its contents are the schemas of the semantically equivalent local relations in the databases. With this representation, the metadata of the global database, local databases and the data of these databases are all representable by using the structure of a relation. The impact of such a representation is that all the elegant features of relational systems can be easily extended to multidatabase systems. A hyperrelational algebra is designed accordingly. This algebra is performed at the multidatabase systems (MDBS) level such that query transformation and optimization is supported on a sound mathematical basis. The major contributions of this paper include: (1) Local relations of various schemas (even though they retain information of the same semantics) can be systematically mapped to hyperrelations. As the structure of a hyperrelation is similar to that of a relation, data manipulation and management tasks (such as design of the global query language and the view mechanism) are greatly facilitated. (2) The hyperrelational algebra provides a sound basis for query transformation and optimization in a MDBS.

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