检索结果-内蒙古大学图书馆

4th IEEE International Conference on BioInspired Processing, BIP 2022

作者： Valverde, Mariana Bonilla Rodriguez, Rodrigo Mora University of Costa Rica Postgraduate Program Sep Master Program on Bioinformatics and Systems Biology San José11501-2060 Costa Rica University of Costa Rica Faculty of Microbiology San José11501-2060 Costa Rica

ISBN: (纸本)9781665470483

In response to force application, biological reactions occur in the periodontal ligament that causes the orthodontic tooth movement. Differential expression of genes such as ALPL, FGF7, PDRM1, and NR4A2 are involved in the exposure to tension or compression forces by contributing to bone remodeling. In this study, a systems biology approach is used in order to identify a modulator of gene expression when mechanical loadings are applied in periodontal ligament cells. We developed a mathematical model of the interaction network of ALPL and FGF7 with several miRNAs and the transcription factor modulators in BioNetUCR, Cytoscape and COPASI software. We found that miR129-2 has a negative control in ALPL, FGF7, NR4A2 and PRDM1 genes, while miRNA192 has a negative control in ALPL and FGF7 genes in compression and tension side. Both miRNAs are proposed for future experimental validation. © 2022 IEEE.

关键词： RNA

来源：评论

学校读者我要写书评

暂无评论

A systems biology Approach to Identify Candidate Targets to Downregulate Angiogenic Gene Expression in Cancer

A Systems Biology Approach to Identify Candidate Targets to ...

引用

International Work Conference on Bio-inspired Intelligence (IWOBI)

作者： Calderon-Gomez Paola Man-Sai Aeón-Chan RA Mora-Rodriguez Master Program on Bioinformatics and Systems Biology University of Costa Rica (UCR) San José Costa Rica Faculty of Microbiology University of Costa Rica (UCR) San José Costa Rica

The control of angiogenesis in cancer has been recognized as a promising therapeutic target for many diseases like cancer. Specifically, the Angiopoietin-2 - Vascular Endothelial Growth Factor system has demonstrated special relevance in the regulation of angiogenesis, highlighting the importance of the complex coordination among vascular signaling molecules [3] for the identification of targets for future anti-angiogenic therapy. Current approaches to regulate the angiogenesis process focus their efforts only on VEGF regulation but this has proven ineffective in many kinds of cancer, prompting the need for further understanding of how the vasculature can be effectively targeted in tumors [9]. Given the complex properties of gene expression in this process, a systems biology approach is required to identify putative candidates to robustly regulate genes involved in angiogenesis. We propose a model with candidate targets to downregulate the angiogenic genes expression. We identified a strong regulation of the AKT1-ANGPT2-KDR axis by miR200B and miR200C. Also, we identified a strong regulation of SRC by miR34a. These candidate miRNAs could therefore have a potential for the development of novel therapeutic strategies against angiogenesis in cancer.

关键词： Biological system modeling Cancer Analytical models Data models Tumors systems biology Mathematical model

来源：评论

学校读者我要写书评

暂无评论

miRNA networks regulating gene expression in response to tension or compression forces in the cells of the periodontal ligament

miRNA networks regulating gene expression in response to ten...

引用

BioInspired Processing (BIP), IEEE International Conference on

作者： Mariana Bonilla Valverde Rodrigo Mora Rodríguez Master Program on Bioinformatics and Systems Biology Postgraduate Program SEP University of Costa Rica 11501-2060 San José Costa Rica Faculty of Microbiology University of Costa Rica 11501-2060 San José Costa Rica

ISBN: (纸本)9781665470490

关键词： systems biology Loading Force Modulation Cells (biology) Bones Software

来源：评论

学校读者我要写书评

暂无评论

A systems biology Approach to Investigate Control Targets of Intracellular Calcium Transients Induced by Clostridium Perfringens Phospholipase C

A Systems Biology Approach to Investigate Control Targets of...

引用

International Work Conference on Bio-inspired Intelligence (IWOBI)

作者： Laura Brenes-Guillén Man-Sai Acón-Chan Rodrigo Mora-Rodríguez Laura Monturiol-Gross Celular and Molecular Biology University of Costa Rica (UCR) San José Costa Rica Master Program on Bioinformatics and Systems Biology University of Costa Rica (UCR) San José Costa Rica Faculty of Microbiology University of Costa Rica (UCR) San José Costa Rica

Clostridium perfringens phospholipase C (CpPLC) plays a key role in the pathogenesis of gas gangrene, an acute and life-threatening infection in humans. CpPLC leads to the unregulated production of second messengers, such as calcium, and activates important signaling pathways like PKC, MEK, and NFkB, inducing ROS production, that leads towards cellular damage. We propose a systems biology approach to identify potential microRNAs which could be used as tools to explore the role of calcium channels in the mechanism of action of CpPLC, and eventually as therapeutic agents that render cells less sensitive to this toxin. Results show that miR19B1 and miR449B are interesting candidate targets which perturbations may affect the expression of genes involved in calcium transport. This approach may be useful to elucidate calcium molecular interactions involved in the CpPLC mechanism of action.

关键词： Calcium Mathematical model Gene expression Network topology Data models systems biology Parameter estimation

来源：评论

学校读者我要写书评

暂无评论

A biocomputational platform for the automated construction of large-scale mathematical models of miRNA-transcription factor networks for studies on gene dosage compensation

A biocomputational platform for the automated construction o...

引用

IEEE Central America and Panama Convention (CONCAPAN)

作者： Acón Man-Sai Siles-Canales Francisco RA Mora-Rodriguez Master Program on Bioinformatics and Systems Biology University of Costa Rica (UCR) San José Costa Rica Faculty of Engineering University of Costa Rica (UCR) San José Costa Rica Faculty of Microbiology University of Costa Rica (UCR) San José Costa Rica

ISBN: (纸本)9781467395793

Cancer complexity and resistance is mediated by cell-to-cell heterogeneity, which is the consequence of the enormous instability of its genetic material. It is unknown how cancer cells are able to withstand the effects of these alterations, while normal cells are typically very sensitive. We hypothesize that cancer requires specific type of stability to survive the enormous chromosomal alterations. This stability may be mediated by a group of genes, whose expression is tightly regulated to maintain viability through a process called gene dosage compensation. This mechanism could be mediated by systems-level properties of complex networks of microRNAs (miRNA) and transcription factors (TF), regulating gene expression despite changes in copy number. Therefore, we designed a biocomputational platform to automatically construct large-scale mathematical models regulating the expression of several candidate genes under dosage compensation. This platform has a broader potential application to other scientific questions involving miRNA and TF networks.

关键词： RNA Proteins DNA Mathematical model Cancer Correlation Gene expression

来源：评论

学校读者我要写书评

暂无评论

K-Means Clustering Model to Discriminate Copper-Resistant Bacteria as Bioremediation Agents

引用

Procedia Computer Science 2021年 179卷 804-812页

作者： Ika Nurlaila Wahyu Irawati Kartika Purwandari Bens Pardamean Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480 Department of Biology Education Faculty of Education Pelita Harapan University Tangerang Indonesia 15811 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Copper (Cu) has been excessively used for some valuable commodities and this creates environmental problems. The inorganic element becomes toxic when presents beyond the recommended tolerated concentration. Bacterial-based remediation is seen to be an excellent tool to overcome it as it reduces the copper contamination without yielding any other forms of contamination. There are some pivotal properties in the bacteria render them being considered as bioremediation agents against coppers contamination, namely bioaccumulation and biosorption. In the present study, we question if these bacteria could be clustered into a strong and representative proximity according to their functional properties. Mostly, bacteria are grouped based on their genetic profiles derived from the 16S rRNA sequencing. We propose that our K-Means clustering model can be employed to identify genetically-unlabelled bacteria. But first, a prominent reference should be developed and we are in this phase. We figured out the K-Means clustering model do not pull the same-genus bacteria into the same cluster. Instead, the model gathers into a proximity those isolates with similarity on a functional characteristic termed minimum inhibitory concentration (MIC), regardless their origins and their hierarchy in taxonomy.

关键词： Copper-Resistant Bacteria K-Means Minimum Inhibitory Concentration

来源：评论

学校读者我要写书评

暂无评论

FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation

引用

Plant physiology 2023年第2期192卷 1449-1465页

作者： Kai-Chun Peng Wei Siao Hsu-Liang Hsieh Institute of Plant Biology College of Life Science National Taiwan University Taipei 106 Taiwan. Department of Plant Biotechnology and Bioinformatics Ghent University 9052 Ghent Belgium. Center for Plant Systems Biology VIB 9052 Ghent Belgium. Department of Life Science College of Life Science National Taiwan University Taipei 106 Taiwan. Master Program in Global Agriculture Technology and Genomic Science National Taiwan University Taipei 106 Taiwan.

Plants can sense the shade from neighboring plants by detecting a reduction of the red:far-red light (R:FR) ratio. Phytochrome B (phyB) is the primary photoreceptor that perceives shade light and regulates jasmonic acid (JA) signaling. However, the molecular mechanisms underlying phyB and JA signaling integration in shade responses remain largely unknown. Here, we show the interaction of phyB and FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT1 (JAR1) in a functional demand manner in Arabidopsis (Arabidopsis thaliana) seedling development. Genetic evidence and interaction studies indicated that phyB and FIN219 synergistically and negatively regulate shade-induced hypocotyl elongation. Moreover, phyB interacted with various isoforms of FIN219 under high and low R:FR light. Methyl jasmonate (MeJA) treatment, FIN219 mutation, and PHYBOE digalactosyldiacylglycerol synthase1-1 (dgd1-1) plants, which show increased levels of JA, altered the patterns of phyB-associated nuclear speckles under the same conditions. Surprisingly, PHYBOE dgd1-1 showed a shorter hypocotyl phenotype than its parental mutants under shade conditions. Microarray assays using PHYBOE and PHYBOE fin219-2 indicated that PHYB overexpression substantially affects defense response-related genes under shade light and coregulates expression of auxin-responsive genes with FIN219. Thus, our findings reveal that phyB substantially crosstalks with JA signaling through FIN219 to modulate seedling development under shade light.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Persistence and dynamic structures of diverse cephalosporinase genes in nontyphoidal Salmonella in cross-sectional surveillance in Taiwan

引用

International Journal of Antimicrobial Agents 2023年第4期62卷 106944-106944页

作者： Lee, Yuarn-Jang Chang, Yu-Chu Lee, I-Hui Ho, Kuo-Hao Fang, Shiuh-Bin Lauderdale, Tsai-Ling Chen, Ting-Wen Chen, Ku-Chung Huang, Chih-Hung Huang, Tzu-Wen Division of Infectious Diseases Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei City Taiwan Division of Infectious Diseases Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Department of Biochemistry and Molecular Cell Biology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan International Ph.D. Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei Taiwan Department of Microbiology and Immunology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei Taiwan Division of Pediatric Gastroenterology and Hepatology Department of Pediatrics Shuang Ho Hospital Taipei Medical University New Taipei City Taiwan Department of Medical Research Shuang Ho Hospital Taipei Medical University New Taipei City Taiwan Department of Pediatrics School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Master Program in Clinical Pharmacogenomics and Pharmacoproteomics College of Pharmacy Taipei Medical University Taipei Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Chemical Engineering and Biotechnology Institute of Chemical Engineering National Taipei University of Technology Taipei Taiwan

Objectives: Nontyphoidal Salmonella (NTS) is a major foodborne pathogen causing from acute gastroenteritis to bacteraemia, particularly in paediatric and elderly patients. Antimicrobial resistance of NTS, especially resistance to extended-spectrum cephalosporins, has emerged over the past decades. Methods: Thirteen NTS isolates resistant to ceftriaxone or cefotaxime were collected from a teaching hospital in Taipei, and another three from a tertiary hospital, in New Taipei City, Taiwan, from September 2018 to December 2019. Ten other archived isolates from 2000 to 2017 were also obtained. Complete genomes of the 26 isolates were obtained. Serovars, sequence types, resistomes, genetic relatedness, and sequence comparison of plasmids were analyzed. Results: Serogroups B, C2 and E were significantly associated with ampicillin resistance. Over 90% of these 26 isolates are susceptible to carbapenems and colistin. Genomic epidemiology of these isolates shows that bla_CMY-2-harbouring isolates in different serovars were prevalent over two decades, presumably resulting from highly mobile IncI1 plasmid harbouring bla_CMY-2. One type of the IncI1 plasmids contained a mobile element, IS26, which might be involved in the acquisition of antimicrobial resistance genes. Two emerging serovars, S. Goldcoast ST358 harbouring bla_CTX-M-55 on IncHI2 plasmids and S. Anatum ST64 harbouring bla_DHA-1 on IncA/C₂ plasmids persisted in Taiwan, possibly through the clonal spread. Integration of complete or partial plasmid sequences into host chromosomes or multiplications of the antimicrobial resistance genes also appears to be mediated by IS26, in the two emerging clones. Conclusion: The dynamic movement of cephalosporinase genes mediated by IS26 in NTS is of great concern. © 2023 The Authors

关键词： Amplification Chromosome integration Epidemiology Foodborne pathogen Insertion sequence Whole-genome sequencing

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：