Creating animal models, why not use the Chinese tree shrew ( Tupaia belangeri chinensis)？

The Chinese tree shrew （Tupaia belangeri chinensis） a squirrel-like and rat-sized mammal, has a wide distribution in Southeast Asia, South and Southwest China and has many unique characteristics that make it suitable for use as an experimental animal. There have been many studies using the tree shrew （Tupaia belangeri） aimed at increasing our understanding of fundamental biological mechanisms and for the modeling of human diseases and therapeutic responses. The recent release of a publicly available annotated genome sequence of the Chinese tree shrew and its genome database （www.treeshrewdb.org） has offered a solid base from which it is possible to elucidate the basic biological properties and create animal models using this species. The extensive characterization of key factors and signaling pathways in the immune and nervous systems has shown that tree shrews possess both conserved and unique features relative to primates. Hitherto, the tree shrew has been successfully used to create animal models for myopia, depression, breast cancer, alcohol-induced or non-alcoholic fatty liver diseases, herpes simplex virus type 1 （HSV-1） and hepatitis C virus （HCV） infections, to name a few. The recent successful genetic manipulation of the tree shrew has opened a new avenue for the wider usage of this animal in biomedical research. In this opinion paper, I attempt to summarize the recent research advances that have used the Chinese tree shrew, with a focus on the new knowledge obtained by using the biological properties identified using the tree shrew genome, a proposal for the genome-based approach for creating animal models, and the genetic manipulation of the tree shrew. With more studies using this species and the application of cutting-edge gene editing techniques, the tree shrew will continue to be under the spot light as a viable animal model for investigating the basis of many different human diseases.

Genome sequencing brought Gossypium biology research into a new era

The first sequenced diploid cotton genome was published in2012 by the group led by the Institute of Cotton Research,Chinese Academy of Agricultural Sciences.Cotton genomics research subsequently entered a period of rapid development.The accumulating data have provided new insights into the evolution and domestication of cotton,the development of important agronomic traits,and strategies

RSMD-repeat searcher and motif detector

The functionality of a gene or a protein depends on codon repeats occurring in it.As a consequence of their vitality in protein function and apparent involvement in causing diseases,an interest in these repeats has developed in recent years.The analysis of genomic and proteomic sequences to identify such repeats requires some algorithmic support from informatics level.Here,we proposed an offline stand-alone toolkit Repeat Searcher and Motif Detector（RSMD）,which uncovers and employs few novel approaches in identification of sequence repeats and motifs to understand their functionality in sequence level and their disease causing tendency.The tool offers various features such as identifying motifs,repeats and identification of disease causing repeats.RSMD was designed to provide an easily understandable graphical user interface（GUI）,for the tool will be predominantly accessed by biologists and various researchers in all platforms of life science.GUI was developed using the scripting language Perl and its graphical module PerlTK.RSMD covers algorithmic foundations of computational biology by combining theory with practice.

Genomics and Applied Biology(GAB)

Genomics and Applie d Biology(ISSN 1925-1602)is an open access and peer reviewed journal published online by Bio Publisher.The journal is committed to publishing and disseminating all the latest and outstanding research articles,letters and reviews in all areas of Genomics and Applied Biology.The range of topics including genomic structure and function,evolutionary and comparative genomics,genomics and bioinformatics。

Genomics and Applied Biology (GAB)

Genomics and Applie d Biology(ISSN 1925-1602)is an open access and peer reviewed journal published online by Bio Publisher.The journal is committed to publishing and disseminating all the latest and outstanding research articles,letters and reviews in all areas of Genomics and Applied Biology.The range of topics including genomic structure

Genomics and Applied Biology(GAB)

Genomics and Applie d Biology(ISSN 1925-1602)is an open access and peer reviewed journal published online by Bio Publisher.The journal is committed to publishing and disseminating all the latest and outstanding research articles,letters and reviews in all areas of Genomics and Applied Biology.The range of topics including genomic structure

Genomics and Applied Biology(GAB)

Genomics and Applie d Biology(ISSN 1925-1602)is an open access and peer reviewed journal published online by Bio Publisher.The journal is committed to publishing and disseminating all the latest and outstanding research articles,letters and reviews in all areas of Genomics and Applied Biology.The range of topics including genomic structure

Web Resources for Model Organism Studies

An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States（NIH; http：//www.nih.gov/science/models/）. We provide a brief description for each database, as well as detail its data source and types, functions, tools, and availability of access. In addition,we also provide a quality assessment about these databases. Significantly, the organism databases instituted in the early 1990s––such as the Mouse Genome Database（MGD）, Saccharomyces Genome Database（SGD）, and Fly Base––have developed into what are now comprehensive, core authority resources. Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.

Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network

A disease phenotype generally reflects various pathobiological processes that interact in a complex network. The highly interconnected nature of the human protein interaction network（interactome） indicates that, at the molecular level, it is difficult to consider diseases as being independent of one another. Recently, genome-wide molecular measurements, data mining and bioinformatics approaches have provided the means to explore human diseases from a molecular basis. The exploration of diseases and a system of disease relationships based on the integration of genome-wide molecular data with the human interactome could offer a powerful perspective for understanding the molecular architecture of diseases. Recently, subnetwork markers have proven to be more robust and reliable than individual biomarker genes selected based on gene expression profiles alone, and achieve higher accuracy in disease classification. We have applied one of these methodologies to idiopathic dilated cardiomyopathy（IDCM） data that we have generated using a microarray and identified significant subnetworks associated with the disease. In this paper, we review the recent endeavours in this direction, and summarize the existing methodologies and computational tools for network-based analysis of complex diseases and molecular relationships among apparently different disorders and human disease network. We also discuss the future research trends and topics of this promising field.