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Clustering Gene expression Data Through Modified Agglomerative M-CURe Hierarchical Algorithm

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Computer Systems Science & engineering 2022年第6期41卷 1027-1041页

作者： e.Kavitha R.Tamilarasan N.Poonguzhali M.K.Jayanthi Kannan A Constituent College of Anna University University College of EngineeringVillupuram605103India A Constituent College of Anna University University College of EngineeringPattukkottai614701India Department of Computer Science and engineering Manakula Vinayagar Institute of TechnologyPuducherry605107India Department of Computer Science engineering Faculty of Engineering and TechnologyJAIN(Deemed-To-Be University)Bangalore562112India

Gene expression refers to the process in which the gene information isused in the functional gene product synthesis. They basically encode the proteinswhich in turn dictate the functionality of the cell. The first step in gene expressionstudy involves the clustering usage. This is due to the reason that biological networks are very complex and the genes volume increases the comprehending challenges along with the data interpretation which itself inhibit vagueness, noise andimprecision. For a biological system to function, the essential cellular moleculesmust interact with its surrounding including RNA, DNA, metabolites and proteins. Clustering methods will help to expose the structures and the patterns inthe original data for taking further decisions. The traditional clustering techniquesinvolve hierarchical, model based, partitioning, density based, grid based and softclustering methods. Though many of these methods provide a reliable output inclustering, they fail to incorporate huge data of gene expressions. Also, thereare statistical issues along with choosing the right method and the choice of dissimilarity matrix when dealing with gene expression data. We propose to use amodified clustering algorithm using representatives (M-CURe) in this workwhich is more robust to outliers as compared to K-means clustering and also ableto find clusters with size variances.

关键词： Clustering gene identifiers representatives dimension reduction

受损的脑血管反应性是不是多发性硬化病人认知功能减退的早期标志物?

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国际医学放射学杂志 2018年第3期 364-364页

作者： A.Metzger e.L.Bars J.Deverdun F.Molino B.Maréchal M.C.Picot 陈祖钦 Department of Neurology University Hospital CenterGui de Chauliac Hospital

摘要目的多发性硬化病人的脑血管反应性与认知功能状态之间的关系尚不清楚。旨在研究多发性硬化病人潜在的脑血管反应性降低,及其与认知功能状态的相关性。方法

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Behavioral effects of social challenges and genomic mechanisms of social priming： What＇s testosterone got to do with it？

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Current Zoology 2014年第6期60卷 791-803页

作者： Kimberly A. ROSVALL Mark e PeTeRSON Indiana University Department of Biology and Center for the Integrative Study of Animal Behavior Bloomington IN 47405 USA Viterbo University Departments of Biology and Mathematics La Crosse WI 54601 USA

Social challenges from rival conspecifics are common in the lives of animals, and changes in an animal＇s social environment can influence physiology and behavior in ways that appear to be adaptive in the face of continued social instability （i.e. social priming）. Recently, it has become clear that testosterone, long thought to be the primary mediator of these effects, may not always change in response to social challenges, an observation that highlights gaps in our understanding of the proximate me- chanisms by which animals respond to their social environment. Here, our goal is to address the degree to which testosterone me- diates organismal responses to social cues. To this end, we review the behavioral and physiological consequences of social chal- lenges, as well as their underlying hormonal and gene regulatory mechanisms. We also present a new case study from a wild songbird, the dark-eyed junco Junco hyemalis, in which we find largely divergent genome-wide transcriptional changes induced by social challenges and testosterone, respectively, in muscle and liver tissue. Our review underscores the diversity of mechani- sms that link the dynamic social environment with an organisms＇ genomic, hormonal, and behavioral state. This diversity among species, and even among tissues within an organism, reveals new insights into the pattern and process by which evolution may alter proximate mechanisms of social priming.

关键词： Social priming challenge hypothesis Aggression Hormonal mechanism Testosterone Genomics

基于MP2RAGe形态测量学评估神经性厌食症相关的脑萎缩

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国际医学放射学杂志 2018年第1期 120-120页

作者： J.Boto G.Gkinis A.Roch T.Kober B.Mareéchal N.Ortiz 柴超 Division of Neuroradiology Geneva University Hospital and Faculty of Medicine of Geneva

摘要目的采用具有自动脑分割功能的双磁化准备快速获得梯度回波(MP2RAGe)MRI序列评估神经性厌食症病人的脑萎缩。材料与方法于2014年8月—2016年12月

关键词：神经性厌食症 MP2RAGe 灰质体积脑萎缩

Prokaryotic expression and Purification of Ds MAPK from Dunaliella salina

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Agricultural Science & Technology 2015年第1期16卷 12-15页

作者：岳文静柴晓杰刘丽颖武天祥刘艺琼农业部北方海水增养殖重点实验室/辽宁省海洋生物资源恢复与生境修复重点实验室大连海洋大学辽宁大连116023

Dunaliella salina is an important model organism for investigating the salt tolerance mechanism of plant. MAPK is the key gene in the molecular pathway of salt tolerance of plant. In this experiment, the open reading frame （ORF） of DsMAPK gene was amplified by PCR. The target fragment was cloned in pGS-21a, a prokaryotic expression vector with GST-tag. The recombinant plasmid pGS-21a- DsMAPK was then transformed into e. coil BL21 （De3）. The expression was induced with IPTG. Then the expression form of the recombinant protein was analyzed. The expression products were purified with GST-SefinoseTM Kit and identified with SDS-PAGe and Western blot. The results showed the recombinant expression vector pGS-21a-DsMAPK was constructed successfully, and the molecular weight of the expressed recombinant protein was as same as expected. Western blot analysis showed the purified recombinant protein could be identified specially by the anti- GST antibody and had a good immunological activity. The successful expression of DsMAPK will lay a basis for the further research on the role of DsMAPK in the salt tolerance mechanism at the protein level.

关键词： Dunaliella salina DsMAPK Prokaryotic expression Purification

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Knockout mouse models of insulin signaling: Relevance past and future

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World Journal of Diabetes 2014年第2期5卷 146-159页

作者： Anne e Bunner P Charukeshi Chandrasekera Neal D Barnard Physicians Committee for Responsible Medicine

Insulin resistance is a hallmark of type 2 diabetes. In an effort to understand and treat this condition, re searchers have used genetic manipulation of mice to uncover insulin signaling pathways and determine the effects of their perturbation. After decades of research much has been learned, but the pathophysiology o insulin resistance in human diabetes remains contro versial, and treating insulin resistance remains a chal lenge. This review will discuss limitations of mouse models lacking select insulin signaling molecule genes In the most influential mouse models, glucose metabo lism differs from that of humans at the cellular, organ and whole-organism levels, and these differences limi the relevance and benefit of the mouse models both in terms of mechanistic investigations and therapeutic development. These differences are due partly to im mutable differences in mouse and human biology, and partly to the failure of genetic modifications to produce an accurate model of human diabetes. Several fac tors often limit the mechanistic insights gained from experimental mice to the particular species and strain including: developmental effects, unexpected meta bolic adjustments, genetic background effects, and technical issues. We conclude that the limitations and weaknesses of genetically modified mouse models of insulin resistance underscore the need for redirection of research efforts toward methods that are more directly relevant to human physiology.

关键词： Insulin resistance Mice Knockout Disease models,Animal Glucose/metabolism Signal transduction

The Genome of Artemisia annua Provides Insight into the evolution of Asteraceae Family and Artemisinin Biosynthesis

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Molecular Plant 2018年第6期11卷 776-788页

作者： Qian Shen Lida Zhang Zhihua Liao Shengyue Wang Tingxiang Yan Pu Shi Meng Liu Xueqing Fu Qifang Pan Yuliang Wang Zongyou Lv Xu Lu Fangyuan Zhang Weimin Jiang Yanan Ma Minghui Chen Xiaolong Hao Ling Li Yueli Tang Gang Lv Yan Zhou Xiaofen Sun Peter e. Brodelius Jocelyn K.C. Rose Kexuan Tang Joint International Research Laboratory of Metabolic & Developmental Sciences Key Laboratory of Urban Agriculture (South) Ministry of Agriculture Plant Biotechnology Research Center Fudan-SJTU-Nottingham Plant Biotechnology R&D Center School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China SWU-TAAHC Medicinal Plant Joint R&D Centre School of Life Sciences Southwest University Chongqing 400715 China Chinese National Human Genome Center at Shanghai Shanghai 201203 China Plant Biology Section School of Integrative Plant Science Cornell University Ithaca NY 14853 USA Department of Chemistry and Biomedical Sciences Linnaeus University 39182 Kalmar Sweden State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 211198 China

Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemi- sinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on compre- hensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the chal- lenge of increasing global demand of artemisinin.

关键词： Artemisia annua artemisinin genome evolution transcriptome metabolic engineering

非创伤性蛛网膜下腔出血的处理:降低碘对比剂剂量的CTA的评估

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国际医学放射学杂志 2012年第5期 477-478页

作者： D.Millon A.L.Derelle P.Omoumi M.Tisserand e.Schmitt S.Foscolo 刘永康 Department of Diagnostic and Therapeutic Neuroradiology Centre Hospitalo Universitaire (CHU) Nancy27 avenue du Maréchal de Lattre de Tassigny54000 NancyFrance

摘要目的评估使用64层螺旋CT以及低剂量对比剂(25mL)在诊断和处理成人非创伤性蛛网膜下腔出血(SAH)的技术性能和诊断价值。方法本研究未在美国本土施行,获得伦理委员会批准。对73例经CT平扫诊断为非创伤性SAH的病人进行颅脑CTA检查。2... 详细信息

摘要目的评估使用64层螺旋CT以及低剂量对比剂(25mL)在诊断和处理成人非创伤性蛛网膜下腔出血(SAH)的技术性能和诊断价值。方法本研究未在美国本土施行,获得伦理委员会批准。对73例经CT平扫诊断为非创伤性SAH的病人进行颅脑CTA检查。2名放射科医师采用2条标准对影像进行评估:动脉强化程度和静脉干扰。各自以血管成像为参考标准来评估其诊断价值(病变检出及治疗决策)。

关键词：创伤性蛛网膜下腔出血 SAH 非创伤性病人 CTA 动脉显影血管成像

全身磁共振扩散成像及表观扩散系数图对弥漫性大B细胞淋巴瘤病人分期的价值

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国际医学放射学杂志 2010年第5期 509-509页

作者： A.Luciani e.Itti T.eI-Gnaoui A.Vignaud A.Rahmouni 颜荣华 Imagerie Médicale AP-HPGroupe Henri-Mondor Albert-ChenevierCHU Henri Mondor51 Avenue du Malréchal de Lattre de Tassigny94010 CréteilFrance

关键词： DWI ADC图呼吸门控弥漫性大B细胞淋巴瘤分期 FDG PeT/CT