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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Interdisciplinary Bio Central
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Journal DOI :
Korean Society for Bioinformatics and Systems Biology
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Volume & Issues
Volume 4, Issue 4 - Dec 2012
Volume 4, Issue 3 - Sep 2012
Volume 4, Issue 2 - Jun 2012
Volume 4, Issue 1 - Mar 2012
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Systemic and Cell-Type Specific Profiling of Molecular Changes in Parkinson`s Disease
Lee, Yunjong ;
Interdisciplinary Bio Central, volume 4, issue 3, 2012, Pages 6.1~6.12
DOI : 10.4051/ibc.2012.4.3.0006
Parkinson`s disease (PD) is a complicated neurodegenerative disorder although it is oftentimes defined by clinical motor symptoms originated from age dependent and progressive loss of dopaminergic neurons in the midbrain. The pathogenesis of PD involves dopaminergic and nondopaminergic neurons in many brain regions and the molecular mechanisms underlying the death of different cell types still remain to be elucidated. There are indications that PD causing disease processes occur in a global scale ranging from DNA to RNA, and proteins. Several PD-associated genes have been reported to play diverse roles in controlling cellular functions in different levels, such as chromatin structure, transcription, processing of mRNA, translational modulation, and posttranslational modification of proteins. The advent of quantitative high throughput screening (HTS) tools makes it possible to monitor systemic changes in DNA, RNA and proteins in PD models. Combined with dopamine neuron isolation or derivation of dopamine neurons from PD patient specific induced pluripotent stem cells (PD iPSCs), HTS techonologies will provide opportunities to draw PD causing sequences of molecular events in pathologically relevant PD samples. Here I discuss previous studies that identified molecular functions in which PD genes are involved, especially those signaling pathways that can be efficiently studied using HTS methodologies. Brief descriptions of quantitative and systemic tools looking at DNA, RNA and proteins will be followed. Finally, I will emphasize the use and potential benefits of PD iPSCs-derived dopaminergic neurons to screen signaling pathways that are initiated by PD linked gene mutations and thus causative for dopaminergic neurodegneration in PD.
Combining Neuroinformatics Databases for Multi-Level Analysis of Brain Disorders
Yu, Ha Sun ; Bang, Joon ; Jo, Yousang ; Lee, Doheon ;
Interdisciplinary Bio Central, volume 4, issue 3, 2012, Pages 7.1~7.8
DOI : 10.4051/ibc.2012.4.3.0007
With the development of many methods of studying the brain, the field of neuroscience has generated large amounts of information obtained from various techniques: imaging techniques, electrophysiological techniques, techniques for analyzing brain connectivity, techniques for getting molecular information of the brain, etc. A plenty of neuroinformatics databases have been made for storing and sharing this useful information and those databases can be publicly accessed by researchers as needed. However, since there are too many neuroinformatics databases, it is difficult to find the appropriate database depending on the needs of researcher. Moreover, many researchers in neuroscience fields are unfamiliar with using neuroinformatics databases for their studies because data is too diverse for neuroscientists to handle this and there is little precedent for using neuroinformatics databases for their research. Therefore, in this article, we review databases in the field of neuroscience according to both their methods for obtaining data and their objectives to help researchers to use databases properly. We also introduce major neuroinformatics databases for each type of information. In addition, to show examples of novel uses of neuroinformatics databases, we represent several studies that combine neuroinformatics databases of different information types and discover new findings. Finally, we conclude our paper with the discussion of potential applications of neuroinformatics databases.
A Simple and Accurate Genotype Analysis of the motor neuron degeneration 2 (mnd2) Mice: an Easy-to-Follow Guideline and Standard Protocol Applicable to Mutant Mouse Model
Shin, Hyun-Ah ; Kim, Goo-Young ; Nam, Min-Kyung ; Goo, Hui-Gwan ; Kang, Seongman ; Rhim, Hyangshuk ;
Interdisciplinary Bio Central, volume 4, issue 3, 2012, Pages 8.1~8.7
DOI : 10.4051/ibc.2012.4.3.0008
The motor neuron degeneration 2 (mnd2) mice carry a point mutation of A to T nucleotide transversion at the serine 276 residue of high temperature requirement A2 (HtrA2), resulting in losses of an AluI restriction enzyme site (5`AGCT3`) and the HtrA2 serine protease activity. Moreover, dysfunctions of HtrA2 are known to be intimately associated with the pathogenesis of neurodegenerative diseases, including Parkinson`s disease. Thus, this mnd2 mouse is an invaluable model for understanding the physiological role of HtrA2 and its pathological role in neurodegenerative diseases. Nevertheless, many molecular and cellular biologists in this field have limited experience in working with mutant mouse models due to the necessity of acquired years of the special techniques and knowledges. Herein, using the mnd2 mouse model as an example, we describe easy-to-use standard protocols for web-based analyses of target genes, such as HtrA2, and a novel approach for simple and accurate PCR-AluI-RFLP-based genotype analysis of mnd2 mice. In addition, band resolution of AluI-RFLP fragments was improved in 12% polyacrylamide gel running in 1X Tris-Glycine SDS buffer. Our study indicates that this PCR-AluI-RFLP genotype analysis method can be easily applied by the molecular and cellular biologist to conduct biomedical science studies using the other mutant mouse models.
Phage Assembly Using APTES-Conjugation of Major Coat p8 Protein for Possible Scaffolds
Kim, Young Jun ; Korkmaz, Nuriye ; Nam, Chang Hoon ;
Interdisciplinary Bio Central, volume 4, issue 3, 2012, Pages 9.1~9.7
DOI : 10.4051/ibc.2012.4.3.0009
Filamentous phages have been in the limelight as a new type of nanomaterial. In this study, genetically and chemically modified fd phage was used to generate a biomimetic phage self-assembly product. Positively charged fd phage (p8-SSG) was engineered by conjugating 3-aminopropyltriethoxysilane (APTES) to hydroxyl groups of two serine amino acid residues introduced at the N-terminus of major coat protein, p8. In particular, formation of a phage network was controlled by changing mixed ratios between wild type fd phage and APTES conjugated fd-SSG phage. Assembled phages showed unique bundle and network like structures. The bacteriophage based self-assembly approach illustrated in this study might contribute to the design of three dimensional microporous structures. In this work, we demonstrated that the positively charged APTES conjugated fd-SSG phages can assemble into microstructures when they are exposed to negatively charged wild-type fd phages through electrostatic interaction. In summary, since we can control the phage self-assembly process in order to obtain bundle or network like structures and since they can be functionalized by means of chemical or genetic modifications, bacteriophages are good candidates for use as bio-compatible scaffolds. Such new type of phage-based artificial 3D architectures can be applied in tuning of cellular structures and functions for tissue engineering studies.
Bacterial Logic Devices Reveal Unexpected Behavior of Frameshift Suppressor tRNAs
Sawyer, Eric M. ; Barta, Cody ; Clemente, Romina ; Conn, Michel ; Davis, Clif ; Doyle, Catherine ; Gearing, Mary ; Ho-Shing, Olivia ; Mooney, Alyndria ; Morton, Jerrad ; Punjabi, Shamita ; Schnoor, Ashley ; Sun, Siya ; Suresh, Shashank ; Szczepanik, Bryce ; Taylor, D. Leland ; Temmink, Annie ; Vernon, William ; Campbell, A. Malcolm ; Heyer, Laurie J. ; Poet, Jeffrey L. ; Eckdahl, Todd T. ;
Interdisciplinary Bio Central, volume 4, issue 3, 2012, Pages 10.1~10.12
DOI : 10.4051/ibc.2012.4.3.0010
Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.