1,721,003 research outputs found
Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport
No full textNewly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane. © 2023 The Author(s)11Nsciescopu
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
단백질 N-말단과 아세포기관의 단백체학적 매핑에 관한 연구
No full text학위논문 (박사) -- 서울대학교 대학원 : 자연과학대학 생명과학부, 2021. 2. 김빛내리.Proteins are one of the fundamental molecules of the living organisms that play a variety of biological roles to maintain life. Many endogenous cellular proteins are tightly regulated from their expression to decay. Following the development of high-throughput proteomic analysis such as liquid chromatography-mass spectrometry (LC-MS), it has become an essential tool for the systematic analysis of protein molecules with the unprecedented scale, time and depth.
This thesis concerns methodological advances in both aspects of protein regulation and localization. First development of a novel method to examine global status of proteolytic events was carried through a new multiplexed N-terminomics method involving selective isobaric labeling of protein N-termini and immunoaffinity capture of the labeled N-terminal peptides. This method allows for not only identification of proteolytic cleavage sites, but also highly multiplexed quantification of proteolytic processing. I profiled a number of potential cleavage sites by signal peptidase and provided experimental confirmation of predicted cleavage sites of signal peptide. Furthermore, the present method uniquely represents the landscape of proteomic proteolytic processing rate during early embryogenesis in Drosophila melanogaster, revealing the underlying mechanism of stringent decay regulation of zygotically expressed proteins during early stages of embryogenesis.
The second part of this thesis describes the development and application of the Massive Identification of Biotinylation Sites (MIBS) method, a newly developed method to identify biotinylation sites at the single amino acid level following intracellular proximity labeling. MIBS was applied to profile the localized proteome of mitochondria associated membrane (MAM) and endoplasmic reticulum. Based on the profiling results, the subcellular and suborganellar localization of identified proteins were systematically defined, as well as systematic topological mapping of transmembrane proteins.
High-throughput proteomics approach by LC-MS can offer an unbiased landscape of proteomes and lead to unexpected findings. In this thesis, I introduced two types of newly developed methodologies that can carry not only global investigation of proteolytically processed sites and subcellular localized proteomes but also quantification of identified proteins of interest. By applying these methods, I discovered several phenomena of proteolytic events and precisely defined subcellular localized proteomes. Further development and improvement of mass spectrometry-based experiment methodologies will offer unique opportunities to discover unexpected proteomic regulations.단백질은 다양한 생물학적 역할을 담당하며 살아있는 유기체의 생명 유지를 위해 매우 중요하다. 세포 내 대다수 단백질들은 발현에서 분해되기까지 매우 엄격한 조절기작에 의해 관리된다. 액체크로마토그래피/질량분석기에 기반한 단백체학 연구방법론은 최근의 눈부신 기술 개발에 힘입어 대규모의 시료를 보다 짧은 시간에 체계적으로 분석할 수 있게 되었으며, 단백체학 연구에 필수적인 기술이 되었다.
이 논문은 단백체의 분해 다이나믹스 및 아세포기관 단백체의 분포위치 매핑이라는 두 방향의 단백체학 방법론 개발에 관한 연구를 담고 있다. 전반부는 단백질 분해 중간체의 동적인 변화를 매핑할 수 있는 새로운 질량분석법을 기술하는데, 단백질의 N-말단에 다중정량분석이 가능하도록 화학적 표지물질을 유도화한 후, 표지된 N-말단 펩티드를 별도로 분리하여 질량분석함으로써 단백질 절단부위의 식별뿐 아니라 단백질 분해 중간체의 정량화를 가능하게 하였다. 그에 따라 여러 단백질의 신호펩티다아제에 의해 절단된 부위를 실험적으로 확인함과 동시에 알려져 있지 않던 새로운 신호절단부위를 예측하고 제시하였다. 또한 초파리 배아의 초기 발생 동안의 단백질 분해 중간체를 확인하고 정량화 함으로 써 단밸질체의 처리 속도를 측정하였고, 배아 발생 극초기 단계에서 배아의 유전체로부터 발현되는 단백질들이 아주 빠르게 분해 되다는 사실을 발견하였다.
후반부에서는 세포 내 근접표지방법에 의해 비오티닐화된 아미노산 잔기를 고도의 정확성과 획기적으로 향상된 효율로 동정할 수 있는 MIBS (Massive Identification of Biotinylation Sites) 분석법의 개발 및 적용에 대한 내용을 기술하였다. MIBS 분석법을 적용하여 미토콘드리아 연관의 막단백질 (MAM) 및 소포체의 단백체를 고해상도로 매핑할 수 있었다. 매핑 결과를 기반으로 식별된 단백질의 세포 내 위치 및 막단백질의 배향을 아세포 수준에서 체계적으로 결정하였다.
이 논문에서는 단백질 분해 처리 부위와 세포 내 위치에 대한 전반적 조사뿐만 아니라 확인된 단백질의 정량화를 수행할 수 있는 두 가지 유형의 새로운 방법론을 제시했다. 질량 분석법 기반 실험 방법론의 추가 개발 및 개선을 통해 기존에 알려지지 않은 단백질체의 성질 및 조절 원리를 발견할 기회가 더욱 늘어날 것으로 보인다.Abstract i
Contents iii
List of Figures vi
List of Tables xi
List of Abbreviations xii
1 Introduction 1
1.1 Proteomics to study cellular protein expression 1
1.1.1 Methods of proteomic profiling 1
1.1.2 LC-MS based systematic, high-throughput approach to analyze protein expression 3
1.1.3 Protein quantification strategies 4
1.2 Post-translational modification regulation and chemical modification of protein 5
2 Multiplexed N-terminomics in embryonic development 7
2.1 Background 7
2.2 Limitations of N-terminomics 8
2.3 Strategy for selective isobaric labeling and enrichment of protein
N-termini 8
2.4 Optimization of protein-level TMT labeling and immunoaffinity capture 13
2.5 Proteome-wide profiling of protein N-termini for Drosophila melanogaster Schneider 2 (S2) cells 19
2.6 Intensity based experimental anotation of SP-cleavage sites 25
2.7 Multiplexed immuno-N-terminomics (miNterm) reveal dynamics of proteolytic processing during early embryonic development in D.melanogaster 28
2.8 Discussion 37
2.9 Long tables for Chapter 2 39
2.10 Methods 44
3 High resolution mapping of subcellular and sub-organellar protein localizations 51
3.1 Background 51
3.2 Limitations of proximity labeling based identification of biotinylated proteins 52
3.3 Development of Massive Identification of biotinylation site (MIBS) 53
3.4 Enhanced mapping of mitochondrial matrix and IMM/IMS using MIBS 58
3.5 Application of MIBS to identifiy the localized proteome at the ER- mitochondrial contact site in live cells 63
3.5.1 Enriched functional protein clusters at the mitochondria- associated membrane (MAM) 71
3.6 Sub-endoplasmic reticulum proteome mapping by MIBS 72
3.6.1 In vivo topology determination of ER membrane proteinsby MIBS 77
3.6.2 High resolution mapping of biotinylation site can support protein structural information 89
3.6.3 Biotinylated tyrosine sites highly overlap with phosphorylation sites 90
3.7 Discussion 94
3.8 Methods 98
3.9 Long tables for Chapter 3 105
4 Conclusion 110
Summary (in Korean) 113
Bibliography 115Docto
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
In vivo profiling of the Zucchini proximal proteome in the Drosophila ovary
No full textPIWI-interacting RNAs (piRNAs) are small RNAs that play a conserved role in genome defense. The piRNA processing pathway is dependent on the sequestration of RNA precursors and protein factors in specific subcellular compartments. Therefore, a highly resolved spatial proteomics approach can help identify the local interactions and elucidate the unknown aspects of piRNA biogenesis. Herein, we performed TurboID proximity labeling to investigate the interactome of Zucchini (Zuc), a key factor of piRNA biogenesis in germline cells and somatic follicle cells of the Drosophila ovary. Quantitative mass spectrometry analysis of biotinylated proteins defined the Zucproximal proteome, including the well-known partners of Zuc. Many of these were enriched in the outer mitochondrial membrane (OMM), where Zuc was specifically localized. The proximal proteome of Zuc showed a distinct set of proteins compared with that of Tom20, a representative OMM protein, indicating that chaperone function-related and endomembrane system/vesicle transport proteins are previously unreported interacting partners of Zuc. The functional relevance of several candidates in piRNA biogenesis was validated by derepression of transposable elements after knockdown. Our results present potential Zuc-interacting proteins, suggesting unrecognized biological processes.11Nsciescopu
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