Developing a bioinformatics framework for proteogenomics

In the last 15 years, since the human genome was first sequenced, genome sequencing and annotation have continued to improve. However, genome annotation has not kept up with the accelerating rate of genome sequencing and as a result there is now a large backlog of genomic data waiting to be interpreted both quickly and accurately. Through advances in proteomics a new field has emerged to help improve genome annotation, termed proteogenomics, which uses peptide mass spectrometry data, enabling the discovery of novel protein coding genes, as well as the refinement and validation of known and putative protein-coding genes. The annotation of genomes relies heavily on ab initio gene prediction programs and/or mapping of a range of RNA transcripts. Although this method provides insights into the gene content of genomes it is unable to distinguish protein-coding genes from putative non-coding RNA genes. This problem is further confounded by the fact that only 5% of the public protein sequence repository at UniProt/SwissProt has been curated and derived from actual protein evidence. This thesis contends that it is critically important to incorporate proteomics data into genome annotation pipelines to provide experimental protein-coding evidence. Although there have been major improvements in proteogenomics over the last decade there are still numerous challenges to overcome. These key challenges include the loss of sensitivity when using inflated search spaces of putative sequences, how best to interpret novel identifications and how best to control for false discoveries. This thesis addresses the existing gap between the use of genomic and proteomic sources for accurate genome annotation by applying a proteogenomics approach with a customised methodology. This new approach was applied within four case studies: a prokaryote bacterium; a monocotyledonous wheat plant; a dicotyledonous grape plant; and human. The key contributions of this thesis are: a new methodology for proteogenomics analysis; 145 suggested gene refinements in Bradyrhizobium diazoefficiens (nitrogen-fixing bacteria); 55 new gene predictions (57 protein isoforms) in Vitis vinifera (grape); 49 new gene predictions (52 protein isoforms) in Homo sapiens (human); and 67 new gene predictions (70 protein isoforms) in Triticum aestivum (bread wheat). Lastly, a number of possible improvements for the studies conducted in this thesis and proteogenomics as a whole have been identified and discussed

Program and Proceedings: The Nebraska Academy of Sciences 1880-2009

PROGRAM FRIDAY, APRIL 17, 2009 REGISTRATION FOR ACADEMY, Lobby of Lecture wing, Olin Hall Aeronautics and Space Science, Olin 249 Collegiate Academy, Biology Session A, Olin B Earth Science, Olin 224 Collegiate Academy, Chemistry and Physics, Session A, Olin 324 Biological and Medical Sciences, Session A, Olin 112 Biological and Medical Sciences, Session B, Smith Callen Conference Center Junior Academy, Senior High REGISTRATION, Olin Hall Lobby NWU Health and Sciences Graduate School Fair, Olin and Smith Curtiss Halls Junior Academy, Senior High Competition, Olin 124, Olin 131 Aeronautics and Space Science, Poster Session, Olin 249 History and Philosophy of Science, Olin 325, combined section Teaching of Science and Math, Olin 325, combined section MAIBEN MEMORIAL LECTURE, OLIN B Dr. Donald Frey, Chair, Department of Family Practice, Creighton University Medical Center LUNCH, PATIO ROOM, STORY STUDENT CENTER (pay and carry tray through cafeteria line, or pay at NAS registration desk) Policy and Program Committee Luncheon, Roundup Room Emeriti Luncheon, Presidents Room Aeronautics Group, Conestoga Room Anthropology, Olin 111 Biological and Medical Sciences, Session C, Olin 112 Biological and Medical Sciences, Session D, Smith Callen Conference Center Chemistry and Physics, Section A, Chemistry, Olin A Chemistry and Physics, Section B, Physics, Planetarium Collegiate Academy, Biology Session A, Olin B Collegiate Academy, Biology Session B, Olin 249 Collegiate Academy, Chemistry and Physics, Session A, Olin 324 Junior Academy, Junior High REGISTRATION, Olin Hall Lobby Junior Academy, Senior High Competition, (Final), Olin 110 Junior Academy, Junior High Competition, Olin 124, Olin 131 NJAS Board/Teacher Meeting, Olin 219 Junior Academy, General Awards Presentations, Smith Callen Conference Center BUSINESS MEETING, OLIN B SOCIAL HOUR for Members, Spouses, and Guests First United Methodist Church, 2723 N 50th Street, Lincoln, NE ANNUAL BANQUET and Presentation of Awards and Scholarships First United Methodist Church, 2723 N 50th Street, Lincoln, N

自然環境下で撮影した作物時系列画像を用いた高速フェノタイピングに関する研究

学位の種別:課程博士University of Tokyo(東京大学

Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u

Structural Investigation of the Complex of Filamin A Repeat 21 with Integrin αIIb and β3 Cytoplasmic Tails – A Potential “Transmission” to Regulate Cell Migration

Cell functions in multi-cellular organisms are strongly depend on the dynamic cooperation between cell adhesion and cytoskeleton reorganization. Integrins, the major cell adhesion receptors, bind to extracellular matrix (ECM) and soluble ligands on the cell surface and link to the actin cytoskeleton inside the cell membrane. In this manner, integrins integrate cell adhesion and cytoskeleton reorganization by acting as a mechanical force transducer and a biochemical signaling hub (Zamir and Geiger 2001). Consequently, integrins are vital for development, immune responses, leukocyte traffic and hemostasis, and a variety of other cellular and physiological processes. Integrins are also are the focal point of many human diseases, including genetic, autoimmune, cardiovascular and others. In terms of the cell-ECM adhesion, integrins can exist in two major states, active, where it binds to appropriate extracellular ligands, and inactive, where it disassociates from extracellular ligands. The cellular pathways that modify the integrin extracellular ligand binding states have been called inside-out integrin signaling while the pathways that are mediated by the extracellular binding have been called outside-in integrin signaling. Although the directions of outside-in and inside-out signaling point to each other, they often happen reciprocally. Rather than just integrins alone accomplishing integrin signaling, numerous proteins are recruited around integrins and are limited to the clearly defined range of focal adhesion that are large molecular complexes containing \u3e100 proteins which link integrins to cytoskeleton (Figure 1) (Zaidel-Bar et al. 2004). Proteins that directly interact with integrins are crucial for understanding integrin signaling. More importantly, proteins that link integrins to the cytoskeleton are responsible for both mechanical forces and biochemical signal transduction, as well as reorganizing the cytoskeleton. Moreover, the modification of integrin ligand binding states is dependent on the linkage t

Structural Investigation of the Complex of Filamin A Repeat 21 with Integrin αIIb and β3 Cytoplasmic Tails – A Potential “Transmission” to Regulate Cell Migration

Cell functions in multi-cellular organisms are strongly depend on the dynamic cooperation between cell adhesion and cytoskeleton reorganization. Integrins, the major cell adhesion receptors, bind to extracellular matrix (ECM) and soluble ligands on the cell surface and link to the actin cytoskeleton inside the cell membrane. In this manner, integrins integrate cell adhesion and cytoskeleton reorganization by acting as a mechanical force transducer and a biochemical signaling hub (Zamir and Geiger 2001). Consequently, integrins are vital for development, immune responses, leukocyte traffic and hemostasis, and a variety of other cellular and physiological processes. Integrins are also are the focal point of many human diseases, including genetic, autoimmune, cardiovascular and others. In terms of the cell-ECM adhesion, integrins can exist in two major states, active, where it binds to appropriate extracellular ligands, and inactive, where it disassociates from extracellular ligands. The cellular pathways that modify the integrin extracellular ligand binding states have been called inside-out integrin signaling while the pathways that are mediated by the extracellular binding have been called outside-in integrin signaling. Although the directions of outside-in and inside-out signaling point to each other, they often happen reciprocally. Rather than just integrins alone accomplishing integrin signaling, numerous proteins are recruited around integrins and are limited to the clearly defined range of focal adhesion that are large molecular complexes containing \u3e100 proteins which link integrins to cytoskeleton (Figure 1) (Zaidel-Bar et al. 2004). Proteins that directly interact with integrins are crucial for understanding integrin signaling. More importantly, proteins that link integrins to the cytoskeleton are responsible for both mechanical forces and biochemical signal transduction, as well as reorganizing the cytoskeleton. Moreover, the modification of integrin ligand binding states is dependent on the linkage t

Accessible software frameworks for reproducible image analysis of host-pathogen interactions

Um die Mechanismen hinter lebensgefährlichen Krankheiten zu verstehen, müssen die zugrundeliegenden Interaktionen zwischen den Wirtszellen und krankheitserregenden Mikroorganismen bekannt sein. Die kontinuierlichen Verbesserungen in bildgebenden Verfahren und Computertechnologien ermöglichen die Anwendung von Methoden aus der bildbasierten Systembiologie, welche moderne Computeralgorithmen benutzt um das Verhalten von Zellen, Geweben oder ganzen Organen präzise zu messen. Um den Standards des digitalen Managements von Forschungsdaten zu genügen, müssen Algorithmen den FAIR-Prinzipien (Findability, Accessibility, Interoperability, and Reusability) entsprechen und zur Verbreitung ebenjener in der wissenschaftlichen Gemeinschaft beitragen. Dies ist insbesondere wichtig für interdisziplinäre Teams bestehend aus Experimentatoren und Informatikern, in denen Computerprogramme zur Verbesserung der Kommunikation und schnellerer Adaption von neuen Technologien beitragen können. In dieser Arbeit wurden daher Software-Frameworks entwickelt, welche dazu beitragen die FAIR-Prinzipien durch die Entwicklung von standardisierten, reproduzierbaren, hochperformanten, und leicht zugänglichen Softwarepaketen zur Quantifizierung von Interaktionen in biologischen System zu verbreiten. Zusammenfassend zeigt diese Arbeit wie Software-Frameworks zu der Charakterisierung von Interaktionen zwischen Wirtszellen und Pathogenen beitragen können, indem der Entwurf und die Anwendung von quantitativen und FAIR-kompatiblen Bildanalyseprogrammen vereinfacht werden. Diese Verbesserungen erleichtern zukünftige Kollaborationen mit Lebenswissenschaftlern und Medizinern, was nach dem Prinzip der bildbasierten Systembiologie zur Entwicklung von neuen Experimenten, Bildgebungsverfahren, Algorithmen, und Computermodellen führen wird

Remote Sensing Data Compression

A huge amount of data is acquired nowadays by different remote sensing systems installed on satellites, aircrafts, and UAV. The acquired data then have to be transferred to image processing centres, stored and/or delivered to customers. In restricted scenarios, data compression is strongly desired or necessary. A wide diversity of coding methods can be used, depending on the requirements and their priority. In addition, the types and properties of images differ a lot, thus, practical implementation aspects have to be taken into account. The Special Issue paper collection taken as basis of this book touches on all of the aforementioned items to some degree, giving the reader an opportunity to learn about recent developments and research directions in the field of image compression. In particular, lossless and near-lossless compression of multi- and hyperspectral images still remains current, since such images constitute data arrays that are of extremely large size with rich information that can be retrieved from them for various applications. Another important aspect is the impact of lossless compression on image classification and segmentation, where a reasonable compromise between the characteristics of compression and the final tasks of data processing has to be achieved. The problems of data transition from UAV-based acquisition platforms, as well as the use of FPGA and neural networks, have become very important. Finally, attempts to apply compressive sensing approaches in remote sensing image processing with positive outcomes are observed. We hope that readers will find our book useful and interestin